6SWD

IC2 body 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: 3.20 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: 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: 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: 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: 12
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: 13
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: 15
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: 19
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: 10
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: 11
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: 14
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: 16
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: 17
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: 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: 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: 9
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

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNA21044Pyrococcus abyssi GE5
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 18
MoleculeChainsLengthOrganism
mRNA520Pyrococcus abyssi GE5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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