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 1.3 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
  • Primary Citation of Related Structures:  

  • 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-tRNAiMet) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this pr ...

    Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNAiMet) 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS3
Z
210Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps3
Find proteins for Q8U004 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U004
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein uL30
3
123Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for P62008 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P62008
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS10
L
102Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps10
Find proteins for P61885 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  P61885
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS13
O
148Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps13
Find proteins for Q8U0E2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U0E2
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS14
P
56Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps14
Find proteins for Q8U013 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U013
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS17
S
67Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps17e
Find proteins for Q8U0U1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U0U1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS19
T
132Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps19
Find proteins for Q8U002 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U002
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS19
U
150Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: rps19e
Find proteins for Q9V0G8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V0G8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS28
X
71Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps28e
Find proteins for Q8U159 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U159
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS27
Y
50Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps27ae
Find proteins for Q8U443 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U443
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS7
H
215Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps7
Find proteins for Q8U0M8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U0M8
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS9
K
135Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps9
Find proteins for Q8U0E7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U0E7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS11
M
137Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps11
Find proteins for Q8U0E3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U0E3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS12
N
147Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: rps12
Find proteins for P61994 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P61994
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS15
Q
158Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps15
Find proteins for Q8TZD9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8TZD9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS17
R
113Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps17
Find proteins for Q8U008 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U008
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS3
A
198Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps3ae
Find proteins for Q8TZE1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8TZE1
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS2
B
202Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps2
Find proteins for Q8U0F0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U0F0
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS24
V
99Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps24e
Find proteins for Q8U442 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U442
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS27
W
63Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps27e
Find proteins for Q8U474 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U474
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS4
D
180Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: rps4
Find proteins for P61992 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P61992
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS4
E
243Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps4e
Find proteins for Q8U011 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U011
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS5
F
236Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps5
Find proteins for Q8U017 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U017
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS6
G
125Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps6e
Find proteins for Q8U3H8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U3H8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein uS8
I
130Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps8
Find proteins for Q8U014 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U014
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eS8
J
127Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rps8e
Find proteins for Q8U1Y5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U1Y5
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein SX
C
57N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein eL41
0
22Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)Mutation(s): 0 
Gene Names: rpl41e
Find proteins for Q8U232 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Go to UniProtKB:  Q8U232
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
aIF1
1
102Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Find proteins for Q57902 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q57902
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
aIF1A
6
113Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 0 
Gene Names: eIF1A (aif1A)
Find proteins for Q9V138 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V138
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
aIF2-gamma
7
415Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2g
Find proteins for Q980A5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q980A5
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
aIF2-beta
8
139Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2b (aif2b)
Find proteins for Q97W59 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W59
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
aIF2-alpha
9
266Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2a (aif2a)
Find proteins for Q97Z79 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97Z79
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNA21518Pyrococcus abyssi GE5
Entity ID: 30
MoleculeChainsLengthOrganism
mRNA526Pyrococcus
Entity ID: 32
MoleculeChainsLengthOrganism
initiator Met-tRNA fMet from E. coli (A1U72 variant)476Escherichia coli
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
GNP
Query on GNP

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

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Download CCD File 
4
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
OMC
Query on OMC
4
RNA LINKINGC10 H16 N3 O8 PC
UNK
Query on UNK
C
L-PEPTIDE LINKINGC4 H9 N O2

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5MU
Query on 5MU
4
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
4
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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