› 8hkx

Electron Microscopy
3.14Å resolution

Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome

Released:
DOI: 10.2210/pdb8hkx/pdb
PDB entry 8hkx coloured by chain, front view.
PDB entry 8hkx coloured by chain, side view.
PDB entry 8hkx coloured by chain, top view.
Source organism: Sulfolobus acidocaldarius DSM 639
Primary publication:
Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Wang YH, Dai H, Zhang L, Wu Y, Wang J, Wang C, Xu CH, Hou H, Yang B, Zhu Y, Zhang X, Zhou J
Nucleic Acids Res (2023)
PMID: 37604686
Related structures: EMD-34862

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 28-mer (preferred)
PDBe Complex ID:
PDB-CPX-226673 (preferred)
Entry contents:
27 distinct polypeptide molecules
1 distinct RNA molecule
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
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
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
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
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
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
UniProt:
  • Canonical: Q4JAP5 (Residues: 2-127; Coverage: 98%)
Gene names: Saci_0758, rps8e
Sequence domains: Ribosomal protein S8e
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
UniProt:
  • Canonical: O05636 (Residues: 4-133; Coverage: 98%)
Gene names: Saci_0582, rps8
Sequence domains: Ribosomal protein S8
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
UniProt:
  • Canonical: Q4JB44 (Residues: 9-123; Coverage: 82%)
Gene names: Saci_0593, rps19
Sequence domains: Ribosomal protein S19
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
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
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 eS31 Chain: S27A
Molecule details ›
Chain: S27A
Length: 54 amino acids
Theoretical weight: 6.26 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAG0 (Residues: 12-65; Coverage: 81%)
Gene names: Saci_0852, rps27ae
Sequence domains: Ribosomal protein S27a
30S ribosomal protein Chain: A
Molecule details ›
Chain: A
Length: 57 amino acids
Theoretical weight: 4.87 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
16s rRNA (1491-MER) Chain: A16S
Molecule details ›
Chain: A16S
Length: 1501 nucleotides
Theoretical weight: 486.92 KDa
Sequence domains: Archaeal small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.14Å
Relevant EMDB volumes: EMD-34862

Quick links

Citations

1 review citation

Predictive modeling and cryo-EM: A synergistic approach to modeling macromolecular structure.
Corum et al. (2024)
1 other article