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Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA, mRNA and aIF1A.

Electron Microscopy
2.6Å resolution
PDB entry 7zai coloured by chain, front view.
PDB entry 7zai coloured by chain, side view.
PDB entry 7zai coloured by chain, top view.
Source organisms:
Assembly composition:
hetero 32-mer (preferred)
Entry contents: 29 distinct polypeptide molecules
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 32-mer
Accessible surface area: 344713.19 Å2
Buried surface area: 189419.0 Å2
Dissociation area: 705.82 Å2
Dissociation energy (ΔGdiss): -0.21 kcal/mol
Dissociation entropy (TΔSdiss): 12.17 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-271269

Macromolecules

Small ribosomal subunit protein eS1
Chain: A
Length: 199 amino acids
Theoretical weight: 22.89 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V2K7 (Residues: 1-199; Coverage: 100%)
Gene names: PAB0035, PYRAB00680, rps3ae
Pfam: Ribosomal S3Ae family
InterPro:
Small ribosomal subunit protein eS1 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS1 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS1 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS2
Chain: B
Length: 202 amino acids
Theoretical weight: 23.03 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V191 (Residues: 1-202; Coverage: 100%)
Gene names: PAB0368, PYRAB05370, rps2
Pfam: Ribosomal protein S2
InterPro:
Small ribosomal subunit protein uS2 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS2 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS2 in PDB entry 7zai, assembly 1, top view.
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Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein
Chain: C
Length: 63 amino acids
Theoretical weight: 7.16 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: G8ZFK7 (Residues: 1-63; Coverage: 100%)
Gene name: PABs13722
Pfam: Small zinc finger protein HVO_2753-like, Zn-binding pocket
InterPro:
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein in PDB entry 7zai, assembly 1, front view.
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein in PDB entry 7zai, assembly 1, side view.
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS4
Chain: D
Length: 180 amino acids
Theoretical weight: 21.38 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61992 (Residues: 1-180; Coverage: 100%)
Gene names: PAB0361, PYRAB05280, rps4
Pfam:
InterPro:
Small ribosomal subunit protein uS4 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS4 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS4 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS4
Chain: E
Length: 243 amino acids
Theoretical weight: 28.25 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1U8 (Residues: 1-243; Coverage: 100%)
Gene names: PAB2397, PYRAB03290, rps4e
Pfam:
InterPro:
Small ribosomal subunit protein eS4 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS4 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS4 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS5
Chain: F
Length: 236 amino acids
Theoretical weight: 26.52 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1V5 (Residues: 1-236; Coverage: 100%)
Gene names: PAB2136, PYRAB03210, rps5
Pfam:
InterPro:
Small ribosomal subunit protein uS5 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS5 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS5 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS6
Chain: G
Length: 125 amino acids
Theoretical weight: 14.03 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9UYS3 (Residues: 1-125; Coverage: 100%)
Gene names: PAB1427, PYRAB14340, rps6e
Pfam: Ribosomal protein S6e
InterPro:
Small ribosomal subunit protein eS6 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS6 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS6 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS7
Chain: H
Length: 215 amino acids
Theoretical weight: 24.66 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V109 (Residues: 1-215; Coverage: 100%)
Gene names: PAB0428, PYRAB06200, rps7
Pfam: Ribosomal protein S7p/S5e
InterPro:
Small ribosomal subunit protein uS7 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS7 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS7 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS8
Chain: I
Length: 130 amino acids
Theoretical weight: 14.77 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1V0 (Residues: 1-130; Coverage: 100%)
Gene names: PAB2131, PYRAB03260, rps8
Pfam: Ribosomal protein S8
InterPro:
Small ribosomal subunit protein uS8 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS8 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS8 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS8
Chain: J
Length: 127 amino acids
Theoretical weight: 14.29 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9UZL4 (Residues: 1-127; Coverage: 100%)
Gene names: PAB0749, PYRAB11320, rps8e
Pfam: Ribosomal protein S8e
InterPro:
Small ribosomal subunit protein eS8 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS8 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS8 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS9
Chain: K
Length: 135 amino acids
Theoretical weight: 15.29 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V195 (Residues: 1-135; Coverage: 100%)
Gene names: PAB0366, PYRAB05330, rps9
Pfam: Ribosomal protein S9/S16
InterPro:
Small ribosomal subunit protein uS9 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS9 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS9 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS10
Chain: L
Length: 102 amino acids
Theoretical weight: 11.8 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V0V6 (Residues: 1-102; Coverage: 100%)
Gene names: PAB0466, PYRAB06840, rps10
Pfam: Ribosomal protein S10p/S20e
InterPro:
Small ribosomal subunit protein uS10 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS10 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS10 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS11
Chain: M
Length: 137 amino acids
Theoretical weight: 14.77 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P62010 (Residues: 1-137; Coverage: 100%)
Gene names: PAB0362, PYRAB05290, rps11
Pfam: Ribosomal protein S11
InterPro:
Small ribosomal subunit protein uS11 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS11 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS11 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS12
Chain: N
Length: 147 amino acids
Theoretical weight: 16.48 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61994 (Residues: 1-147; Coverage: 100%)
Gene names: PAB0427, PYRAB06190, rps12
Pfam: Ribosomal protein S12/S23
InterPro:
Small ribosomal subunit protein uS12 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS12 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS12 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS13
Chain: O
Length: 148 amino acids
Theoretical weight: 16.99 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1A0 (Residues: 1-148; Coverage: 100%)
Gene names: PAB0360, PYRAB05270, rps13
Pfam: Ribosomal protein S13/S18
InterPro:
Small ribosomal subunit protein uS13 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS13 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS13 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS14
Chain: P
Length: 56 amino acids
Theoretical weight: 6.64 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P62012 (Residues: 1-56; Coverage: 100%)
Gene names: PAB7080, PYRAB03270, rps14
Pfam: Ribosomal protein S14p/S29e
InterPro:
Small ribosomal subunit protein uS14 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS14 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS14 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS15
Chain: Q
Length: 158 amino acids
Theoretical weight: 18.7 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V2K9 (Residues: 1-158; Coverage: 100%)
Gene names: PAB0033, PYRAB00660, rps15
Pfam:
InterPro:
Small ribosomal subunit protein uS15 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS15 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS15 in PDB entry 7zai, assembly 1, top view.
Molecule details ›

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Small ribosomal subunit protein uS17
Chain: R
Length: 113 amino acids
Theoretical weight: 13.36 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1U5 (Residues: 1-113; Coverage: 100%)
Gene names: PAB2127, PYRAB03320, rps17
Pfam: Ribosomal protein S17
InterPro:
Small ribosomal subunit protein uS17 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS17 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS17 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS17
Chain: S
Length: 67 amino acids
Theoretical weight: 8.06 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V0G0 (Residues: 1-67; Coverage: 100%)
Gene names: PAB7207, PYRAB08290, rps17e
Pfam: Ribosomal S17
InterPro:
Small ribosomal subunit protein eS17 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS17 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS17 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS19
Chain: T
Length: 132 amino acids
Theoretical weight: 15.31 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1T9 (Residues: 1-132; Coverage: 100%)
Gene names: PAB2123, PYRAB03380, rps19
Pfam: Ribosomal protein S19
InterPro:
Small ribosomal subunit protein uS19 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS19 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS19 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS19
Chain: U
Length: 150 amino acids
Theoretical weight: 17.42 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V0G8 (Residues: 1-150; Coverage: 100%)
Gene names: PAB1813, PYRAB08210, rps19e
Pfam: Ribosomal protein S19e
InterPro:
Small ribosomal subunit protein eS19 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS19 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS19 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS24
Chain: V
Length: 99 amino acids
Theoretical weight: 11.8 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9UY20 (Residues: 1-99; Coverage: 100%)
Gene names: PAB3419, PYRAB16880, rps24e
Pfam: Ribosomal protein S24e
InterPro:
Small ribosomal subunit protein eS24 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS24 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS24 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS27
Chain: W
Length: 65 amino acids
Theoretical weight: 7.19 KDa
Source organism: Pyrococcus abyssi
UniProt:
  • Canonical: Q9UXZ3 (Residues: 1-65; Coverage: 100%)
Gene names: PAB7435, PYRAB17140, rps27e
Pfam: Ribosomal protein S27
InterPro:
Small ribosomal subunit protein eS27 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS27 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS27 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS28
Chain: X
Length: 71 amino acids
Theoretical weight: 8.1 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61029 (Residues: 1-71; Coverage: 100%)
Gene names: PAB7165, PYRAB06760, rps28e
Pfam: Ribosomal protein S28e
InterPro:
Small ribosomal subunit protein eS28 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS28 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS28 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS31
Chain: Y
Length: 51 amino acids
Theoretical weight: 5.99 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61238 (Residues: 1-51; Coverage: 100%)
Gene names: PAB3419a, PYRAB16885, rps27ae
Pfam: Ribosomal protein S27a
InterPro:
Small ribosomal subunit protein eS31 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS31 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS31 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein uS3
Chain: Z
Length: 210 amino acids
Theoretical weight: 23.47 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1U1 (Residues: 1-210; Coverage: 100%)
Gene names: PAB2125, PYRAB03360, rps3
Pfam:
InterPro:
Small ribosomal subunit protein uS3 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein uS3 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein uS3 in PDB entry 7zai, assembly 1, top view.
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Small ribosomal subunit protein eS32
Chain: 0
Length: 36 amino acids
Theoretical weight: 4.91 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U232 (Residues: 1-36; Coverage: 97%)
Gene names: PF1018, rpl41e
Small ribosomal subunit protein eS32 in PDB entry 7zai, assembly 1, front view.
Small ribosomal subunit protein eS32 in PDB entry 7zai, assembly 1, side view.
Small ribosomal subunit protein eS32 in PDB entry 7zai, assembly 1, top view.
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Large ribosomal subunit protein eL8
Chain: 3
Length: 123 amino acids
Theoretical weight: 13.44 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P62008 (Residues: 1-123; Coverage: 100%)
Gene names: PAB0460, PYRAB06750, rpl7ae
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
InterPro:
Large ribosomal subunit protein eL8 in PDB entry 7zai, assembly 1, front view.
Large ribosomal subunit protein eL8 in PDB entry 7zai, assembly 1, side view.
Large ribosomal subunit protein eL8 in PDB entry 7zai, assembly 1, top view.
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Translation initiation factor 1A
Chain: 6
Length: 134 amino acids
Theoretical weight: 15.34 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V138 (Residues: 1-113; Coverage: 100%)
Gene names: PAB2441, PYRAB05910, aif1A, eIF1A
Pfam: Translation initiation factor 1A / IF-1
InterPro:
Translation initiation factor 1A in PDB entry 7zai, assembly 1, front view.
Translation initiation factor 1A in PDB entry 7zai, assembly 1, side view.
Translation initiation factor 1A in PDB entry 7zai, assembly 1, top view.
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RNA chain 2
Name: 16S ribosomal RNA
Representative chains: 2
Length: 1497 nucleotides
Theoretical weight: 487.99 KDa
Rfam: Archaeal small subunit ribosomal RNA
16S ribosomal RNA in PDB entry 7zai, assembly 1, front view.
16S ribosomal RNA in PDB entry 7zai, assembly 1, side view.
16S ribosomal RNA in PDB entry 7zai, assembly 1, top view.
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RNA chain 5
Name: Messenger RNA
Representative chains: 5
Length: 25 nucleotides
Theoretical weight: 8.06 KDa
Messenger RNA in PDB entry 7zai, assembly 1, front view.
Messenger RNA in PDB entry 7zai, assembly 1, side view.
Messenger RNA in PDB entry 7zai, assembly 1, top view.
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RNA chain 4
Name: tRNA-MET
Representative chains: 4
Length: 77 nucleotides
Theoretical weight: 24.83 KDa
Rfam: tRNA
tRNA-MET in PDB entry 7zai, assembly 1, front view.
tRNA-MET in PDB entry 7zai, assembly 1, side view.
tRNA-MET in PDB entry 7zai, assembly 1, top view.
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