› 8wq2

Electron Microscopy
4.1Å resolution

Structural basis of translation inhibition by a valine tRNA-derived fragment

Released:
DOI: 10.2210/pdb8wq2/pdb
PDB entry 8wq2 coloured by chain, front view.
PDB entry 8wq2 coloured by chain, side view.
PDB entry 8wq2 coloured by chain, top view.
Source organism: Sulfolobus acidocaldarius DSM 639
Primary publication:
Structural basis of translation inhibition by a valine tRNA-derived fragment.
Wu Y, Ni MT, Wang YH, Wang C, Hou H, Zhang X, Zhou J
OpenAccess logo Life Sci Alliance 7 (2024)
PMID: 38599770
Related structures: EMD-37733

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-517511 (preferred)
Entry contents:
26 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (28 distinct):
Small ribosomal subunit protein uS2 Chain: AS2P
Molecule details ›
Chain: AS2P
Length: 196 amino acids
Theoretical weight: 22.47 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39478 (Residues: 28-223; Coverage: 87%)
Gene names: Saci_0088, nbp1, rps2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS4 Chain: AS4E
Molecule details ›
Chain: AS4E
Length: 240 amino acids
Theoretical weight: 27.34 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05634 (Residues: 2-241; Coverage: 98%)
Gene names: Saci_0585, rps4e
Sequence domains:
Small ribosomal subunit protein uS4 Chain: AS4P
Molecule details ›
Chain: AS4P
Length: 166 amino acids
Theoretical weight: 19.44 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39467 (Residues: 3-168; Coverage: 94%)
Gene names: Saci_0081, rps4
Sequence domains:
Small ribosomal subunit protein uS5 Chain: AS5P
Molecule details ›
Chain: AS5P
Length: 204 amino acids
Theoretical weight: 22.78 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05641 (Residues: 11-214; Coverage: 95%)
Gene names: Saci_0577, rps5
Sequence domains:
Small ribosomal subunit protein eS6 Chain: AS6E
Molecule details ›
Chain: AS6E
Length: 105 amino acids
Theoretical weight: 11.48 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAI1 (Residues: 109-213; Coverage: 49%)
Gene names: Saci_0831, rps6e
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein eS8 Chain: AS8E
Molecule details ›
Chain: AS8E
Length: 126 amino acids
Theoretical weight: 14.11 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAP5 (Residues: 2-127; Coverage: 98%)
Gene names: Saci_0758, rps8e
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS11 Chain: S11P
Molecule details ›
Chain: S11P
Length: 128 amino acids
Theoretical weight: 13.65 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39469 (Residues: 5-132; Coverage: 97%)
Gene names: Saci_0082, rps11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: S12P
Molecule details ›
Chain: S12P
Length: 143 amino acids
Theoretical weight: 15.7 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P11524 (Residues: 3-145; Coverage: 97%)
Gene names: Saci_0688, rps12
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS15 Chain: S15P
Molecule details ›
Chain: S15P
Length: 149 amino acids
Theoretical weight: 17.44 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAI3 (Residues: 1-149; Coverage: 97%)
Gene names: Saci_0829, rps15
Sequence domains:
Small ribosomal subunit protein uS17 Chain: S17P
Molecule details ›
Chain: S17P
Length: 111 amino acids
Theoretical weight: 12.6 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB49 (Residues: 3-113; Coverage: 97%)
Gene names: Saci_0588, rps17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein eS24 Chain: S24E
Molecule details ›
Chain: S24E
Length: 96 amino acids
Theoretical weight: 10.77 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAF9 (Residues: 9-104; Coverage: 81%)
Gene names: Saci_0853, rps24e
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27 Chain: S27E
Molecule details ›
Chain: S27E
Length: 59 amino acids
Theoretical weight: 6.58 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4J9B1 (Residues: 1-59; Coverage: 89%)
Gene names: Saci_1276, rps27e
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS1 Chain: S3AE
Molecule details ›
Chain: S3AE
Length: 189 amino acids
Theoretical weight: 21.88 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB17 (Residues: 9-197; Coverage: 96%)
Gene names: Saci_0620, rps3ae
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS3 Chain: AS3P
Molecule details ›
Chain: AS3P
Length: 201 amino acids
Theoretical weight: 22.4 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB46 (Residues: 2-202; Coverage: 87%)
Gene names: Saci_0591, rps3
Sequence domains:
Small ribosomal subunit protein uS7 Chain: AS7P
Molecule details ›
Chain: AS7P
Length: 193 amino acids
Theoretical weight: 21.86 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P17198 (Residues: 3-195; Coverage: 99%)
Gene names: Saci_0686, rps7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9 Chain: AS9P
Molecule details ›
Chain: AS9P
Length: 136 amino acids
Theoretical weight: 15.64 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39468 (Residues: 3-138; Coverage: 99%)
Gene names: Saci_0086, rps9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: S10P
Molecule details ›
Chain: S10P
Length: 100 amino acids
Theoretical weight: 11.78 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P17199 (Residues: 3-102; Coverage: 98%)
Gene names: Saci_0684, rps10
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS13 Chain: S13P
Molecule details ›
Chain: S13P
Length: 147 amino acids
Theoretical weight: 17.14 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39470 (Residues: 3-149; Coverage: 87%)
Gene names: Saci_0080, rps13
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: S14P
Molecule details ›
Chain: S14P
Length: 52 amino acids
Theoretical weight: 6.19 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05635 (Residues: 3-54; Coverage: 96%)
Gene names: Saci_0583, rps14
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS17 Chain: S17E
Molecule details ›
Chain: S17E
Length: 62 amino acids
Theoretical weight: 7.34 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAX5 (Residues: 2-63; Coverage: 76%)
Gene names: Saci_0670, rps17e
Sequence domains: Ribosomal S17
Small ribosomal subunit protein eS19 Chain: S19E
Molecule details ›
Chain: S19E
Length: 150 amino acids
Theoretical weight: 17.56 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4J8U1 (Residues: 3-152; Coverage: 97%)
Gene names: Saci_1469, rps19e
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein uS19 Chain: S19P
Molecule details ›
Chain: S19P
Length: 115 amino acids
Theoretical weight: 13.8 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB44 (Residues: 9-123; Coverage: 82%)
Gene names: Saci_0593, rps19
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein eS31 Chain: S27A
Molecule details ›
Chain: S27A
Length: 54 amino acids
Theoretical weight: 6.26 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAG0 (Residues: 12-65; Coverage: 81%)
Gene names: Saci_0852, rps27ae
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein eS28 Chain: S28E
Molecule details ›
Chain: S28E
Length: 63 amino acids
Theoretical weight: 7.09 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAV1 (Residues: 19-81; Coverage: 75%)
Gene names: Saci_0698, rps28e
Sequence domains: Ribosomal protein S28e
Large ribosomal subunit protein eL8 Chain: SL7A
Molecule details ›
Chain: SL7A
Length: 123 amino acids
Theoretical weight: 13.35 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4J8P1 (Residues: 4-126; Coverage: 98%)
Gene names: Saci_1520, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS8 Chain: AS8P
Molecule details ›
Chain: AS8P
Length: 130 amino acids
Theoretical weight: 14.62 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
Expression system: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05636 (Residues: 4-133; Coverage: 98%)
Gene names: Saci_0582, rps8
Sequence domains: Ribosomal protein S8
RNA (1328-MER) Chain: A16S
Molecule details ›
Chain: A16S
Length: 1501 nucleotides
Theoretical weight: 486.92 KDa
Sequence domains: Archaeal small subunit ribosomal RNA
RNA (26-MER) Chain: VTRF
Molecule details ›
Chain: VTRF
Length: 26 nucleotides
Theoretical weight: 8.41 KDa

Ligands and Environments

1 bound ligand:
Ligand UNK 57 x UNK
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-37733
Expression system: Sulfolobus acidocaldarius DSM 639

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