7Z34

Structure of pre-60S particle bound to DRG1(AFG2).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1.

Prattes, M.Grishkovskaya, I.Hodirnau, V.V.Hetzmannseder, C.Zisser, G.Sailer, C.Kargas, V.Loibl, M.Gerhalter, M.Kofler, L.Warren, A.J.Stengel, F.Haselbach, D.Bergler, H.

(2022) Nat Struct Mol Biol 29: 942-953

  • DOI: https://doi.org/10.1038/s41594-022-00832-5
  • Primary Citation of Related Structures:  
    7Z11, 7Z34

  • PubMed Abstract: 

    The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.


  • Organizational Affiliation

    Institute of Molecular Biosciences, University of Graz, Graz, Austria.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATPase family gene 2 protein780Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AFG2DRG1YLR397CL8084.16
EC: 3.6.4.10
UniProt
Find proteins for P32794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32794 
Go to UniProtKB:  P32794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32794
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Probable metalloprotease ARX1E [auth 4]593Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3
UniProt
Find proteins for Q03862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03862 
Go to UniProtKB:  Q03862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03862
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AF [auth A]254Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX45 
Go to UniProtKB:  P0CX45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX45
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3G [auth B]387Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14126 
Go to UniProtKB:  P14126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14126
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AH [auth C]362Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10664 
Go to UniProtKB:  P10664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10664
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5I [auth D]297Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26321 
Go to UniProtKB:  P26321
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26321
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-AJ [auth E]176Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02326 
Go to UniProtKB:  Q02326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02326
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AK [auth F]244Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05737 
Go to UniProtKB:  P05737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05737
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AL [auth G]256Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17076 
Go to UniProtKB:  P17076
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17076
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AM [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05738 
Go to UniProtKB:  P05738
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05738
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Bud site selection protein 20N [auth I]166Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q08004 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08004 
Go to UniProtKB:  Q08004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-AO [auth J]174Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C0W9 
Go to UniProtKB:  P0C0W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0W9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28P [auth K]149Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02406 
Go to UniProtKB:  P02406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02406
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AQ [auth L]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12690 
Go to UniProtKB:  Q12690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12690
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AR [auth M]138Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36105 
Go to UniProtKB:  P36105
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36105
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AS [auth N]204Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05748 
Go to UniProtKB:  P05748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05748
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AT [auth O]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26784 
Go to UniProtKB:  P26784
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26784
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AU [auth P]184Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05740 
Go to UniProtKB:  P05740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05740
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AV [auth Q]186Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX49 
Go to UniProtKB:  P0CX49
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX49
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AW [auth R]189Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX82 
Go to UniProtKB:  P0CX82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX82
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AX [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX23 
Go to UniProtKB:  P0CX23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX23
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AY [auth T]160Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02753 
Go to UniProtKB:  Q02753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02753
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AZ [auth U]121Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05749 
Go to UniProtKB:  P05749
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05749
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AAA [auth V]137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX41 
Go to UniProtKB:  P0CX41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX41
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome assembly factor MRT4BA [auth W]236Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P33201 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33201 
Go to UniProtKB:  P33201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33201
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25CA [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04456 
Go to UniProtKB:  P04456
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04456
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ADA [auth Y]127Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05743 
Go to UniProtKB:  P05743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-AEA [auth Z]136Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C2H6 
Go to UniProtKB:  P0C2H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C2H6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12-AFA [auth a]165Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX53 
Go to UniProtKB:  P0CX53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX53
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar GTP-binding protein 1GA [auth b]647Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02892 
Go to UniProtKB:  Q02892
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02892
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30HA [auth c]105Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14120 
Go to UniProtKB:  P14120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14120
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AIA [auth d]113Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C2H8 
Go to UniProtKB:  P0C2H8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C2H8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32JA [auth e]130Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38061 
Go to UniProtKB:  P38061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38061
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AKA [auth f]107Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05744 
Go to UniProtKB:  P05744
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05744
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-ALA [auth g]121Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P87262 
Go to UniProtKB:  P87262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP87262
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AMA [auth h]120Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX84 
Go to UniProtKB:  P0CX84
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX84
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ANA [auth i]100Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05745 
Go to UniProtKB:  P05745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05745
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AOA [auth j]88Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49166 
Go to UniProtKB:  P49166
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49166
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38PA [auth k]78Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49167 
Go to UniProtKB:  P49167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49167
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39QA [auth l]51Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04650 
Go to UniProtKB:  P04650
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04650
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29TA [auth o]59Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05747 
Go to UniProtKB:  P05747
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05747
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-AUA [auth p]92Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX25 
Go to UniProtKB:  P0CX25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX25
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-AVA [auth q]106Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX27 
Go to UniProtKB:  P0CX27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CX27
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein NSA2WA [auth r]261Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40078 
Go to UniProtKB:  P40078
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40078
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome biogenesis protein RLP24YA [auth u]199Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07915 
Go to UniProtKB:  Q07915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07915
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal export protein NMD3ZA [auth v]518Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38861 
Go to UniProtKB:  P38861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38861
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6CB [auth y]245Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12522 
Go to UniProtKB:  Q12522
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12522
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0642 protein YBL028CDB [auth z]106Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P38202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38202 
Go to UniProtKB:  P38202
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38202
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown peptideEB [auth 0]19Saccharomyces cerevisiae S288CMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinFB [auth oC]170Saccharomyces cerevisiae S288CMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
35S pre-ribosomal RNAB [auth 1]3,396Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth 2]121Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth 3]158Saccharomyces cerevisiae S288C
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS

Download Ideal Coordinates CCD File 
GB [auth Aa]
HB [auth Aa]
JB [auth m]
KB [auth m]
LB [auth n]
GB [auth Aa],
HB [auth Aa],
JB [auth m],
KB [auth m],
LB [auth n],
MB [auth n],
NB [auth t],
OB [auth w],
PB [auth w],
QB [auth w],
RB [auth x]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
IB [auth b]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIXv.1.20.1-4487-000

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustria--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 2.0: 2023-07-19
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary