6SWC

IC2B model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.

Coureux, P.D.Lazennec-Schurdevin, C.Bourcier, S.Mechulam, Y.Schmitt, E.

(2020) Commun Biol 3: 58-58

  • DOI: 10.1038/s42003-020-0780-0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA i Met . Here, we dete ...

    Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA i Met . Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA i Met complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N 4 -acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.


    Organizational Affiliation

    Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128, Palaiseau, cedex, France. emmanuelle.schmitt@polytechnique.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
202Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps2PYRAB05370PAB0368
Find proteins for Q9V191 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V191

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Zn-ribbon RNA-binding protein involved in translation
C
63Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PABs13722
Find proteins for G8ZFK7 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  G8ZFK7

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
180Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4PYRAB05280PAB0361
Find proteins for P61992 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P61992

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4e
E
243Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4ePYRAB03290PAB2397
Find proteins for Q9V1U8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1U8

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
F
236Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps5PYRAB03210PAB2136
Find proteins for Q9V1V5 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1V5

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6e
G
125Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps6ePYRAB14340PAB1427
Find proteins for Q9UYS3 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UYS3

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
H
215Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps7PYRAB06200PAB0428
Find proteins for Q9V109 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V109

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
I
130Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps8PYRAB03260PAB2131
Find proteins for Q9V1V0 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1V0

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8e
J
127Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps8ePYRAB11320PAB0749
Find proteins for Q9UZL4 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UZL4

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
K
135Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps9PYRAB05330PAB0366
Find proteins for Q9V195 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V195

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
L
102Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps10PYRAB06840PAB0466
Find proteins for Q9V0V6 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V0V6

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
M
137Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps11PYRAB05290PAB0362
Find proteins for P62010 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P62010

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
N
147Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps12PYRAB06190PAB0427
Find proteins for P61994 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P61994

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
O
148Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps13PYRAB05270PAB0360
Find proteins for Q9V1A0 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1A0

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
P
56Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps14PYRAB03270PAB7080
Find proteins for P62012 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P62012

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
Q
158Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps15PYRAB00660PAB0033
Find proteins for Q9V2K9 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2K9

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17e
S
67Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps17ePYRAB08290PAB7207
Find proteins for Q9V0G0 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V0G0

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19e
U
150Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19ePYRAB08210PAB1813
Find proteins for Q9V0G8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V0G8

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24e
V
99Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps24ePYRAB16880PAB3419
Find proteins for Q9UY20 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UY20

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27e
W
65Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps27ePYRAB17140PAB7435
Find proteins for Q9UXZ3 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9UXZ3

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27ae
Y
51Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps27aePYRAB16885PAB3419a
Find proteins for P61238 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P61238

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
Z
210Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps3PYRAB03360PAB2125
Find proteins for Q9V1U1 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1U1

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein aL41
0
36Pyrococcus abyssi GE5Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
3
123Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rpl7aePYRAB06750PAB0460
Find proteins for P62008 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P62008

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 1A
6
113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eIF1Aaif1APYRAB05910PAB2441
Find proteins for Q9V138 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V138

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit gamma
7
415Pyrococcus abyssi GE5Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit alpha
9
266Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: eif2aaif2aSSO1050
Find proteins for Q97Z79 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97Z79

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
R
113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps17PYRAB03320PAB2127
Find proteins for Q9V1U5 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1U5

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3Ae
A
199Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps3aePYRAB00680PAB0035
Find proteins for Q9V2K7 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2K7

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
T
132Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19PYRAB03380PAB2123
Find proteins for Q9V1T9 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V1T9

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28e
X
71Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps28ePYRAB06760PAB7165
Find proteins for P61029 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  P61029

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit beta
8
139Pyrococcus abyssi GE5Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 30
MoleculeChainsLengthOrganism
mRNA520Pyrococcus abyssi GE5

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal rRNA21497Pyrococcus abyssi GE5

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Entity ID: 31
MoleculeChainsLengthOrganism
initiator Met-tRNA fMet from E. coli (A1U72 variant)476Escherichia coli
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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

Download CCD File 
4
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
C, F, P, R, W
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
2, 4, 5, 7
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-17-CE11-0037

Revision History 

  • Version 1.0: 2020-02-19
    Type: Initial release