7ZAI image
Deposition Date 2022-03-22
Release Date 2022-07-13
Last Version Date 2024-11-13
Entry Detail
PDB ID:
7ZAI
Keywords:
Title:
Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA, mRNA and aIF1A.
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L41e
Gene (Uniprot):rpl41e
Chain IDs:BA (auth: 0)
Chain Length:36
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: 2)
Chain Length:1497
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7Ae
Gene (Uniprot):rpl7ae
Chain IDs:CA (auth: 3)
Chain Length:123
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polyribonucleotide
Molecule:tRNA-MET
Chain IDs:EA (auth: 4)
Chain Length:77
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:DA (auth: 5)
Chain Length:25
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:Translation initiation factor 1A
Gene (Uniprot):eIF1A
Chain IDs:FA (auth: 6)
Chain Length:134
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3Ae
Gene (Uniprot):rps3ae
Chain IDs:B (auth: A)
Chain Length:199
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rps2
Chain IDs:C (auth: B)
Chain Length:202
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:Zn-ribbon RNA-binding protein involved in translation
Gene (Uniprot):PABs13722
Chain IDs:D (auth: C)
Chain Length:63
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rps4
Chain IDs:E (auth: D)
Chain Length:180
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4e
Gene (Uniprot):rps4e
Chain IDs:F (auth: E)
Chain Length:243
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rps5
Chain IDs:G (auth: F)
Chain Length:236
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6e
Gene (Uniprot):rps6e
Chain IDs:H (auth: G)
Chain Length:125
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rps7
Chain IDs:I (auth: H)
Chain Length:215
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rps8
Chain IDs:J (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8e
Gene (Uniprot):rps8e
Chain IDs:K (auth: J)
Chain Length:127
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rps9
Chain IDs:L (auth: K)
Chain Length:135
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rps10
Chain IDs:M (auth: L)
Chain Length:102
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rps11
Chain IDs:N (auth: M)
Chain Length:137
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rps12
Chain IDs:O (auth: N)
Chain Length:147
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rps13
Chain IDs:P (auth: O)
Chain Length:148
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rps14
Chain IDs:Q (auth: P)
Chain Length:56
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rps15
Chain IDs:R (auth: Q)
Chain Length:158
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rps17
Chain IDs:S (auth: R)
Chain Length:113
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17e
Gene (Uniprot):rps17e
Chain IDs:T (auth: S)
Chain Length:67
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rps19
Chain IDs:U (auth: T)
Chain Length:132
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19e
Gene (Uniprot):rps19e
Chain IDs:V (auth: U)
Chain Length:150
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S24e
Gene (Uniprot):rps24e
Chain IDs:W (auth: V)
Chain Length:99
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S27e
Gene (Uniprot):rps27e
Chain IDs:X (auth: W)
Chain Length:65
Number of Molecules:1
Biological Source:Pyrococcus abyssi
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S28e
Gene (Uniprot):rps28e
Chain IDs:Y (auth: X)
Chain Length:71
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S27ae
Gene (Uniprot):rps27ae
Chain IDs:Z (auth: Y)
Chain Length:51
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rps3
Chain IDs:AA (auth: Z)
Chain Length:210
Number of Molecules:1
Biological Source:Pyrococcus abyssi GE5
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU EA U modified residue
5MC A C modified residue
5MU EA U modified residue
6MZ A A modified residue
A2M A A modified residue
B8H A U modified residue
H2U EA U modified residue
LHH A C modified residue
MA6 A A modified residue
OMC A C modified residue
OMG A G modified residue
OMU A U modified residue
PSU EA U modified residue
UR3 A U modified residue
Primary Citation
Role of aIF5B in archaeal translation initiation.
Nucleic Acids Res. 50 6532 6548 (2022)
PMID: 35694843 DOI: 10.1093/nar/gkac490

Abstact

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.

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