7ZAH

Cryo-EM structure of an archaeal aIF5B bound to the ssu translation initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Role of aIF5B in archaeal translation initiation.

Kazan, R.Bourgeois, G.Lazennec-Schurdevin, C.Larquet, E.Mechulam, Y.Coureux, P.D.Schmitt, E.

(2022) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkac490
  • Primary Citation of Related Structures:  
    7YYP, 7YZN, 7ZAG, 7ZAH, 7ZAI, 7ZHG, 7ZKI

  • PubMed Abstract: 
  • In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained ...

    In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AeB [auth A]199Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps3aePYRAB00680PAB0035
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2C [auth B]202Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps2PYRAB05370PAB0368
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Zn-ribbon RNA-binding protein involved in translationD [auth C]63Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PABs13722
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4E [auth D]180Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4PYRAB05280PAB0361
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4eF [auth E]243Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps4ePYRAB03290PAB2397
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5G [auth F]236Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps5PYRAB03210PAB2136
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6eH [auth G]125Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps6ePYRAB14340PAB1427
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7I [auth H]215Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps7PYRAB06200PAB0428
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Entity ID: 10
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30S ribosomal protein S8J [auth I]130Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps8PYRAB03260PAB2131
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8eK [auth J]127Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps8ePYRAB11320PAB0749
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9L [auth K]135Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps9PYRAB05330PAB0366
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Entity ID: 13
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30S ribosomal protein S10M [auth L]102Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps10PYRAB06840PAB0466
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Entity ID: 14
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30S ribosomal protein S11N [auth M]137Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps11PYRAB05290PAB0362
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Entity ID: 15
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30S ribosomal protein S12O [auth N]147Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps12PYRAB06190PAB0427
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Entity ID: 16
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30S ribosomal protein S13P [auth O]148Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps13PYRAB05270PAB0360
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZQ [auth P]56Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps14PYRAB03270PAB7080
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Entity ID: 18
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30S ribosomal protein S15R [auth Q]158Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps15PYRAB00660PAB0033
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Entity ID: 19
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30S ribosomal protein S17S [auth R]113Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps17PYRAB03320PAB2127
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Entity ID: 20
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30S ribosomal protein S17eT [auth S]67Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps17ePYRAB08290PAB7207
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19U [auth T]132Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19PYRAB03380PAB2123
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19eV [auth U]150Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps19ePYRAB08210PAB1813
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S24eW [auth V]99Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps24ePYRAB16880PAB3419
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Entity ID: 24
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30S ribosomal protein S27eX [auth W]65Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps27ePYRAB17140PAB7435
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Entity ID: 25
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30S ribosomal protein S28eY [auth X]65Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps28ePYRAB06760PAB7165
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Entity ID: 26
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30S ribosomal protein S27aeZ [auth Y]51Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps27aePYRAB16885PAB3419a
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AA [auth Z]210Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rps3PYRAB03360PAB2125
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L41eBA [auth 0]36Pyrococcus abyssi GE5Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeCA [auth 3]123Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: rpl7aePYRAB06750PAB0460
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 1AFA [auth 6]134Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: eIF1Aaif1APYRAB05910PAB2441
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 5BGA [auth 7]619Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: infBPYRAB11390PAB0755
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth 2]1497Pyrococcus abyssi GE5
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Entity ID: 30
MoleculeChainsLengthOrganismImage
mRNADA [auth 5]22Pyrococcus abyssi GE5
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Entity ID: 31
MoleculeChainsLengthOrganismImage
tRNA-METEA [auth 4]77Pyrococcus abyssi GE5
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

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

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WC [auth 4]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

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MC [auth C],
NC [auth C],
OC [auth F],
SC [auth P],
TC [auth R],
MC [auth C],
NC [auth C],
OC [auth F],
SC [auth P],
TC [auth R],
UC [auth W]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth 2],
AC [auth 2],
BB [auth 2],
BC [auth 2],
CB [auth 2],
AB [auth 2],
AC [auth 2],
BB [auth 2],
BC [auth 2],
CB [auth 2],
CC [auth 2],
DB [auth 2],
DC [auth 2],
EB [auth 2],
EC [auth 2],
FB [auth 2],
FC [auth 2],
GB [auth 2],
GC [auth 2],
HA [auth 2],
HB [auth 2],
HC [auth 2],
IA [auth 2],
IB [auth 2],
IC [auth 2],
JA [auth 2],
JB [auth 2],
JC [auth 2],
KA [auth 2],
KB [auth 2],
KC [auth 2],
LA [auth 2],
LB [auth 2],
LC [auth 2],
MA [auth 2],
MB [auth 2],
NA [auth 2],
NB [auth 2],
OA [auth 2],
OB [auth 2],
PA [auth 2],
PB [auth 2],
PC [auth F],
QA [auth 2],
QB [auth 2],
QC [auth K],
RA [auth 2],
RB [auth 2],
RC [auth M],
SA [auth 2],
SB [auth 2],
TA [auth 2],
TB [auth 2],
UA [auth 2],
UB [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 5],
WA [auth 2],
WB [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 4],
YA [auth 2],
YB [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release