5JBH

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-IN conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cryo-EM study of start codon selection during archaeal translation initiation.

Coureux, P.D.Lazennec-Schurdevin, C.Monestier, A.Larquet, E.Cladiere, L.Klaholz, B.P.Schmitt, E.Mechulam, Y.

(2016) Nat Commun 7: 13366-13366

  • DOI: 10.1038/ncomms13366
  • Primary Citation of Related Structures:  
    5JBH, 5JB3

  • PubMed Abstract: 
  • Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA i Met ) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear ...

    Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA i Met ) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. In the first state, the TC is bound to the ribosome in a relaxed conformation with the tRNA oriented out of the P site. In the second state, the tRNA is accommodated within the peptidyl (P) site and the TC becomes constrained. This constraint is compensated by codon/anticodon base pairing, whereas in the absence of a start codon, aIF2 contributes to swing out the tRNA. This spring force concept highlights a mechanism of codon/anticodon probing by the initiator tRNA directly assisted by aIF2.


    Organizational Affiliation

    Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau cedex, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein uS3B [auth Z]210Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 3
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50S ribosomal protein uL30C [auth 3]123Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rpl7aePYRAB06750PAB0460
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein uS10D [auth L]102Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 5
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30S ribosomal protein uS13E [auth O]148Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 6
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30S ribosomal protein uS14F [auth P]56Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 7
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30S ribosomal protein eS17G [auth S]67Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 8
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30S ribosomal protein uS19H [auth T]132Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 9
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30S ribosomal protein eS19I [auth U]150Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19ePYRAB08210PAB1813
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Entity ID: 10
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30S ribosomal protein eS28J [auth X]71Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 11
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30S ribosomal protein eS27K [auth Y]50Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 12
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30S ribosomal protein uS7L [auth H]215Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 13
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30S ribosomal protein uS9M [auth K]135Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 14
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30S ribosomal protein uS11N [auth M]137Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 15
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30S ribosomal protein uS12O [auth N]147Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps12PYRAB06190PAB0427
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Entity ID: 16
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30S ribosomal protein uS15P [auth Q]158Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 17
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30S ribosomal protein uS17Q [auth R]113Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 18
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30S ribosomal protein uS3R [auth A]198Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 19
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30S ribosomal protein uS2S [auth B]202Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 20
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30S ribosomal protein eS24T [auth V]99Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 21
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30S ribosomal protein eS27U [auth W]63Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 22
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30S ribosomal protein uS4V [auth D]180Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4PYRAB05280PAB0361
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Entity ID: 23
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30S ribosomal protein eS4W [auth E]243Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 24
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30S ribosomal protein uS5X [auth F]236Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 25
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30S ribosomal protein eS6Y [auth G]125Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 26
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30S ribosomal protein uS8Z [auth I]130Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 27
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30S ribosomal protein eS8AA [auth J]127Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 28
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30S ribosomal protein SXBA [auth C]57Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 29
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30S ribosomal protein eL41CA [auth 0]22Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
aIF1EA [auth 1]102Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
aIF1AGA [auth 6]113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eIF1Aaif1APYRAB05910PAB2441
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
aIF2-gammaHA [auth 7]415Pyrococcus abyssi GE5Mutation(s): 0 
EC: 3.6.5.3
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Entity ID: 35
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aIF2-betaIA [auth 8]139Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 36
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aIF2-alphaJA [auth 9]266Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth 2]1518Pyrococcus abyssi GE5
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Entity ID: 30
MoleculeChainsLengthOrganismImage
mRNADA [auth 5]26Pyrococcus
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Entity ID: 32
MoleculeChainsLengthOrganismImage
initiator Met-tRNA fMet from E. coli (A1U72 variant)FA [auth 4]76Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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MA [auth 7]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MET
Query on MET

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KA [auth 4]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

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NA [auth 8]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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LA [auth 7]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Data collection
  • Version 1.2: 2017-02-08
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.5: 2019-12-11
    Changes: Other