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: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4eE243Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4ePYRAB03290PAB2397
Find proteins for Q9V1U8 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5F236Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps5PYRAB03210PAB2136
Find proteins for Q9V1V5 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8I130Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps8PYRAB03260PAB2131
Find proteins for Q9V1V0 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8eJ127Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps8ePYRAB11320PAB0749
Find proteins for Q9UZL4 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13O148Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps13PYRAB05270PAB0360
Find proteins for Q9V1A0 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19T132Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19PYRAB03380PAB2123
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S24eV99Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps24ePYRAB16880PAB3419
Find proteins for Q9UY20 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27aeY51Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps27aePYRAB16885PAB3419a
Find proteins for P61238 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3Z210Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps3PYRAB03360PAB2125
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit gamma7415Pyrococcus abyssi GE5Mutation(s): 0 
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 alpha9266Saccharolobus solfataricus P2Mutation(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: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9K135Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps9PYRAB05330PAB0366
Find proteins for Q9V195 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10L102Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps10PYRAB06840PAB0466
Find proteins for Q9V0V6 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 14
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: 15
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: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type ZP56Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps14PYRAB03270PAB7080
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15Q158Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps15PYRAB00660PAB0033
Find proteins for Q9V2K9 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17R113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps17PYRAB03320PAB2127
Find proteins for Q9V1U5 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AeA199Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps3aePYRAB00680PAB0035
Find proteins for Q9V2K7 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17eS67Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps17ePYRAB08290PAB7207
Find proteins for Q9V0G0 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 22
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: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S27eW65Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps27ePYRAB17140PAB7435
Find proteins for Q9UXZ3 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S28eX71Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps28ePYRAB06760PAB7165
Find proteins for P61029 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein aL41036Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q8U232 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae3123Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rpl7aePYRAB06750PAB0460
Find proteins for P62008 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2B202Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps2PYRAB05370PAB0368
Find proteins for Q9V191 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 32
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 beta8139Pyrococcus abyssi GE5Mutation(s): 0 
Find proteins for Q97W59 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Zn-ribbon RNA-binding protein involved in translationC63Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PABs13722
Find proteins for G8ZFK7 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4D180Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4PYRAB05280PAB0361
Find proteins for P61992 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6eG125Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps6ePYRAB14340PAB1427
Find proteins for Q9UYS3 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7H215Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps7PYRAB06200PAB0428
Find proteins for Q9V109 (Pyrococcus abyssi (strain GE5 / Orsay))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal rRNA21497Pyrococcus abyssi GE5
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Entity ID: 30
MoleculeChainsLengthOrganism
mRNA520Pyrococcus 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

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

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

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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

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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