6RM3

Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.

Barandun, J.Hunziker, M.Vossbrinck, C.R.Klinge, S.

(2019) Nat Microbiol 4: 1798-1804

  • DOI: https://doi.org/10.1038/s41564-019-0514-6
  • Primary Citation of Related Structures:  
    6RM3

  • PubMed Abstract: 

    Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance 1-3 , and are significant opportunistic parasites of humans 4 . They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle 5 , rudimentary mitochondria and the smallest known eukaryotic genomes 5-7 . Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome 8-10 . In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.


  • Organizational Affiliation

    Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY, USA. jonas.barandun@umu.se.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL2C [auth LA0]237Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uS2D [auth SA0]264Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uL15E [auth LAA]148Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eS26F [auth SAA]104Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL3G [auth LB0]384Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS1H [auth SB0]237Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eL29I [auth LBB]55Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eS27J [auth SBB]94Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uL4K [auth LC0]334Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uS5L [auth SC0]237Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL30M [auth LCC]108Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eS28N [auth SCC]67Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uL18O [auth LD0]295Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS3P [auth SD0]215Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL31Q [auth LDD]111Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uS14R [auth SDD]68Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL6S [auth LE0]172Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eS4T [auth SE0]262Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eL32U [auth LEE]139Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eS30V [auth SEE]60Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
uL30W [auth LF0]239Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS7X [auth SF0]189Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL33Y [auth LFF]98Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eS31Z [auth SFF]151Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL8AA [auth LG0]200Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS6BA [auth SG0]217Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eL34CA [auth LGG]106Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1DA [auth SGG]337Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uL6EA [auth LH0]186Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS7FA [auth SH0]161Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uL29GA [auth LHH]122Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
uL16HA [auth LI0]217Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eS8IA [auth SI0]166Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL36JA [auth LII]95Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
uL5KA [auth LJ0]171Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
uS4LA [auth SJ0]189Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL37MA [auth LJJ]93Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL13NA [auth LL0]162Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uS17OA [auth SL0]158Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL39PA [auth LLL]52Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL14QA [auth LM0]105Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL40RA [auth LMM]127Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eS12SA [auth SM0]131Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
eL15TA [auth LN0]204Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
uS15UA [auth SN0]149Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
MDF2VA [auth LNN]160Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
MDF1WA [auth SNN]168Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uL13XA [auth LO0]192Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
uS11YA [auth SO0]135Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
eL42ZA [auth LOO]103Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
uL22AB [auth LP0]169Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uS19BB [auth SP0]143Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
eL43CB [auth LPP]89Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
eL18DB [auth LQ0]193Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
uS9EB [auth SQ0]155Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
eL19FB [auth LR0]175Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
eS17GB [auth SR0]119Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
eL20HB [auth LS0]180Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS13IB [auth SS0]160Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
eL21JB [auth LT0]160Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
eS19KB [auth ST0]133Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
eL22LB [auth LU0]107Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS10MB [auth SU0]101Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uL14NB [auth LV0]146Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
eS21OB [auth SV0]67Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eL24PB [auth LW0]91Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS8QB [auth SW0]127Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
uL23RB [auth LX0]102Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
uS12SB [auth SX0]140Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
msL1TB [auth LXX]73Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
uL24UB [auth LY0]139Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
eS24VB [auth SY0]133Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eL27WB [auth LZ0]126Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eS25XB [auth SZ0]123Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eS10YB [auth SK0]99Vairimorpha necatrixMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth S60]1,244Vairimorpha necatrix
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth L70]119Vairimorpha necatrix
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 78
MoleculeChains LengthOrganismImage
23S rRNAZB [auth L50]2,484Vairimorpha necatrix
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AE [auth SDD]
BE [auth LGG]
CE [auth LJJ]
EE [auth LMM]
FE [auth SNN]
AE [auth SDD],
BE [auth LGG],
CE [auth LJJ],
EE [auth LMM],
FE [auth SNN],
GE [auth LOO],
HE [auth LPP],
YD [auth SAA],
ZD [auth SBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth S60]
AD [auth S60]
AF [auth L50]
AG [auth L50]
AH [auth L50]
AC [auth S60],
AD [auth S60],
AF [auth L50],
AG [auth L50],
AH [auth L50],
AI [auth L50],
AJ [auth L50],
BC [auth S60],
BD [auth S60],
BF [auth L50],
BG [auth L50],
BH [auth L50],
BI [auth L50],
CC [auth S60],
CD [auth S60],
CF [auth L50],
CG [auth L50],
CH [auth L50],
CI [auth L50],
DC [auth S60],
DD [auth S60],
DE [auth LJJ],
DF [auth L50],
DG [auth L50],
DH [auth L50],
DI [auth L50],
EC [auth S60],
ED [auth S60],
EF [auth L50],
EG [auth L50],
EH [auth L50],
EI [auth L50],
FC [auth S60],
FD [auth S60],
FF [auth L50],
FG [auth L50],
FH [auth L50],
FI [auth L50],
GC [auth S60],
GD [auth S60],
GF [auth L50],
GG [auth L50],
GH [auth L50],
GI [auth L50],
HC [auth S60],
HD [auth S60],
HF [auth L50],
HG [auth L50],
HH [auth L50],
HI [auth L50],
IC [auth S60],
ID [auth S60],
IE [auth LV0],
IF [auth L50],
IG [auth L50],
IH [auth L50],
II [auth L50],
JC [auth S60],
JD [auth S60],
JE [auth L50],
JF [auth L50],
JG [auth L50],
JH [auth L50],
JI [auth L50],
KC [auth S60],
KD [auth S60],
KE [auth L50],
KF [auth L50],
KG [auth L50],
KH [auth L50],
KI [auth L50],
LC [auth S60],
LD [auth S60],
LE [auth L50],
LF [auth L50],
LG [auth L50],
LH [auth L50],
LI [auth L50],
MC [auth S60],
MD [auth S60],
ME [auth L50],
MF [auth L50],
MG [auth L50],
MH [auth L50],
MI [auth L50],
NC [auth S60],
ND [auth S60],
NE [auth L50],
NF [auth L50],
NG [auth L50],
NH [auth L50],
NI [auth L50],
OC [auth S60],
OD [auth S60],
OE [auth L50],
OF [auth L50],
OG [auth L50],
OH [auth L50],
OI [auth L50],
PC [auth S60],
PD [auth S60],
PE [auth L50],
PF [auth L50],
PG [auth L50],
PH [auth L50],
PI [auth L50],
QC [auth S60],
QD [auth S60],
QE [auth L50],
QF [auth L50],
QG [auth L50],
QH [auth L50],
QI [auth L50],
RC [auth S60],
RD [auth S60],
RE [auth L50],
RF [auth L50],
RG [auth L50],
RH [auth L50],
RI [auth L50],
SC [auth S60],
SD [auth S60],
SE [auth L50],
SF [auth L50],
SG [auth L50],
SH [auth L50],
SI [auth L50],
TC [auth S60],
TD [auth S60],
TE [auth L50],
TF [auth L50],
TG [auth L50],
TH [auth L50],
TI [auth L50],
UC [auth S60],
UD [auth S60],
UE [auth L50],
UF [auth L50],
UG [auth L50],
UH [auth L50],
UI [auth L50],
VC [auth S60],
VD [auth S60],
VE [auth L50],
VF [auth L50],
VG [auth L50],
VH [auth L50],
VI [auth L50],
WC [auth S60],
WD [auth S60],
WE [auth L50],
WF [auth L50],
WG [auth L50],
WH [auth L50],
WI [auth L50],
XC [auth S60],
XD [auth L70],
XE [auth L50],
XF [auth L50],
XG [auth L50],
XH [auth L50],
XI [auth L50],
YC [auth S60],
YE [auth L50],
YF [auth L50],
YG [auth L50],
YH [auth L50],
YI [auth L50],
ZC [auth S60],
ZE [auth L50],
ZF [auth L50],
ZG [auth L50],
ZH [auth L50],
ZI [auth L50]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1DP2GM123459
Swiss National Science FoundationSwitzerland155515

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references