5JB3

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-REMOTE 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 1.3 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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
30S ribosomal protein S11M137Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps11PYRAB05290PAB0362
Find proteins for P62010 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12N147Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps12PYRAB06190PAB0427
Find proteins for P61994 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15Q158Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8TZD9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17PR113Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U008 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AeA198Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8TZE1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2B202Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U0F0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24eV99Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27eW63Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3Z210Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4D180Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4PYRAB05280PAB0361
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4eE243Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5F236Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6eG125Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U3H8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8I130Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U014 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8eJ127Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U1Y5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein SXC57Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae3123Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10L102Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for P61885 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13O148Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U0E2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type ZP56Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17eS67Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U0U1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19T132Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U002 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19eU150Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19ePYRAB08210PAB1813
Find proteins for Q9V0G8 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28eX71Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U159 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27aeY50Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U443 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7H215Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U0M8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9K135Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U0E7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eL41022Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U232 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Protein translation factor SUI1 homolog1102Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: MJ0463
Find proteins for Q57902 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 1A6113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eIF1Aaif1APYRAB05910PAB2441
Find proteins for Q9V138 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit gamma7415Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eif2gSSO0412
EC: 3.6.5.3
Find proteins for Q980A5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit beta8139Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eif2baif2bSSO2381
Find proteins for Q97W59 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit alpha9266Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eif2aaif2aSSO1050
Find proteins for Q97Z79 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 30
MoleculeChainsLengthOrganism
initiator Met-tRNA fMet from E. coli (A1U72 variant)476Escherichia coli

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Entity ID: 31
MoleculeChainsLengthOrganism
mRNA526Pyrococcus abyssi GE5

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNA21519Pyrococcus abyssi GE5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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

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7
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

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8
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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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 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence, Data collection, Other