3JCN

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association: Initiation Complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.

Sprink, T.Ramrath, D.J.Yamamoto, H.Yamamoto, K.Loerke, J.Ismer, J.Hildebrand, P.W.Scheerer, P.Burger, J.Mielke, T.Spahn, C.M.

(2016) Sci Adv 2: e1501502-e1501502

  • DOI: https://doi.org/10.1126/sciadv.1501502
  • Primary Citation of Related Structures:  
    3JCJ, 3JCN

  • PubMed Abstract: 

    Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.


  • Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Escherichia coliMutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L33B [auth 1]55Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]46Escherichia coliMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L35D [auth 3]65Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L36E [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 8
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50S ribosomal protein L2H [auth C]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3I [auth D]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4J [auth E]201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5K [auth F]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6L [auth G]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9M [auth H]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L11N [auth I]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13O [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14P [auth K]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15Q [auth L]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16R [auth M]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17S [auth N]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18T [auth O]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19U [auth P]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20V [auth Q]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21W [auth R]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22X [auth S]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23Y [auth T]100Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth U]104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25AA [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L27BA [auth W]85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28CA [auth X]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29DA [auth Y]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30EA [auth Z]59Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2GA [auth b]890Escherichia coliMutation(s): 0 
Gene Names: infBgicDssyGb3168JW3137
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30S ribosomal protein S3HA [auth c]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S2IA [auth d]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S5JA [auth f]159Escherichia coliMutation(s): 0 
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30S ribosomal protein S4KA [auth g]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S7LA [auth h]179Escherichia coliMutation(s): 0 
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30S ribosomal protein S6MA [auth i]135Escherichia coliMutation(s): 0 
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30S ribosomal protein S9NA [auth j]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S8OA [auth k]130Escherichia coliMutation(s): 0 
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30S ribosomal protein S11PA [auth l]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S10QA [auth m]102Escherichia coliMutation(s): 0 
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30S ribosomal protein S13RA [auth n]118Escherichia coliMutation(s): 0 
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30S ribosomal protein S12SA [auth o]124Escherichia coliMutation(s): 0 
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30S ribosomal protein S15TA [auth p]89Escherichia coliMutation(s): 0 
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30S ribosomal protein S14UA [auth q]101Escherichia coliMutation(s): 0 
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30S ribosomal protein S17VA [auth r]84Escherichia coliMutation(s): 0 
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30S ribosomal protein S16WA [auth s]82Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth t]92Escherichia coliMutation(s): 0 
UniProt
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UniProt GroupP0A7U3
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth u]75Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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UniProt GroupP0A7T7
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21AB [auth w]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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UniProt GroupP68679
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BB [auth x]87Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains LengthOrganismImage
23S ribosomal RNAF [auth A]2,904Escherichia coli
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S ribosomal RNAG [auth B]120Escherichia coli
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S ribosomal RNAFA [auth a]1,542Escherichia coli
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Entity ID: 52
MoleculeChains LengthOrganismImage
tRNAZA [auth v]77Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
messenger RNACB [auth z]6Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
DB [auth b]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
FME
Query on FME

Download Ideal Coordinates CCD File 
EB [auth v]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection