› 8hkv

Electron Microscopy
4.94Å resolution

Cryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome

Released:
DOI: 10.2210/pdb8hkv/pdb
PDB entry 8hkv coloured by chain, front view.
PDB entry 8hkv coloured by chain, side view.
PDB entry 8hkv 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-34861

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 39-mer (preferred)
PDBe Complex ID:
PDB-CPX-226664 (preferred)
Entry contents:
35 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (37 distinct):
Large ribosomal subunit protein uL2 Chain: AL2P
Molecule details ›
Chain: AL2P
Length: 234 amino acids
Theoretical weight: 24.88 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB43 (Residues: 2-235; Coverage: 98%)
Gene names: Saci_0594, rpl2
Sequence domains:
Large ribosomal subunit protein uL3 Chain: AL3P
Molecule details ›
Chain: AL3P
Length: 339 amino acids
Theoretical weight: 38.19 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB40 (Residues: 4-342; Coverage: 99%)
Gene names: Saci_0597, rpl3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: AL4P
Molecule details ›
Chain: AL4P
Length: 251 amino acids
Theoretical weight: 27.36 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB41 (Residues: 9-259; Coverage: 94%)
Gene names: Saci_0596, rpl4
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: AL5P
Molecule details ›
Chain: AL5P
Length: 168 amino acids
Theoretical weight: 19.1 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P41202 (Residues: 8-175; Coverage: 94%)
Gene names: Saci_0584, rpl5
Sequence domains:
Large ribosomal subunit protein uL6 Chain: AL6P
Molecule details ›
Chain: AL6P
Length: 181 amino acids
Theoretical weight: 20.31 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05637 (Residues: 4-184; Coverage: 96%)
Gene names: Saci_0581, rpl6
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein eL20 Chain: ALX0
Molecule details ›
Chain: ALX0
Length: 76 amino acids
Theoretical weight: 8.93 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P38613 (Residues: 4-79; Coverage: 88%)
Gene names: Saci_1464, rlx, rpl18a, rpl20e, rplX
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein uL16 Chain: L10E
Molecule details ›
Chain: L10E
Length: 164 amino acids
Theoretical weight: 18.67 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JC84 (Residues: 4-167; Coverage: 93%)
Gene names: Saci_0176, rpl10e
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL13 Chain: L13P
Molecule details ›
Chain: L13P
Length: 140 amino acids
Theoretical weight: 15.81 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39473 (Residues: 8-147; Coverage: 95%)
Gene names: Saci_0085, rpl13
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein eL14 Chains: L141, L142
Molecule details ›
Chains: L141, L142
Length: 86 amino acids
Theoretical weight: 9.56 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAJ9 (Residues: 3-88; Coverage: 90%)
Gene names: Saci_0813, rpl14e
Sequence domains: KOW motif
Large ribosomal subunit protein uL14 Chain: L14P
Molecule details ›
Chain: L14P
Length: 134 amino acids
Theoretical weight: 14.71 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB50 (Residues: 5-138; Coverage: 97%)
Gene names: Saci_0587, rpl14
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL15 Chain: L15E
Molecule details ›
Chain: L15E
Length: 169 amino acids
Theoretical weight: 20.18 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB20 (Residues: 4-172; Coverage: 78%)
Gene names: Saci_0617, rpl15e
Sequence domains: Ribosomal L15
Large ribosomal subunit protein eL18 Chain: L18E
Molecule details ›
Chain: L18E
Length: 112 amino acids
Theoretical weight: 12.75 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P39474 (Residues: 6-117; Coverage: 95%)
Gene names: Saci_0084, rpl18e
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein uL18 Chain: L18P
Molecule details ›
Chain: L18P
Length: 193 amino acids
Theoretical weight: 21.77 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05640 (Residues: 2-194; Coverage: 98%)
Gene names: Saci_0578, rpl18
Sequence domains: Ribosomal large subunit proteins 60S L5, and 50S L18
Large ribosomal subunit protein eL19 Chain: L19E
Molecule details ›
Chain: L19E
Length: 144 amino acids
Theoretical weight: 17.11 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05639 (Residues: 2-145; Coverage: 96%)
Gene names: Saci_0579, rpl19e
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein uL22 Chain: L22P
Molecule details ›
Chain: L22P
Length: 150 amino acids
Theoretical weight: 17.36 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB45 (Residues: 6-155; Coverage: 96%)
Gene names: Saci_0592, rpl22
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: L23P
Molecule details ›
Chain: L23P
Length: 81 amino acids
Theoretical weight: 9.26 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB42 (Residues: 2-82; Coverage: 99%)
Gene names: Saci_0595, rpl23
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein eL24 Chain: L24E
Molecule details ›
Chain: L24E
Length: 54 amino acids
Theoretical weight: 6.34 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAV2 (Residues: 5-58; Coverage: 87%)
Gene names: Saci_0697, rpl24e
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL24 Chain: L24P
Molecule details ›
Chain: L24P
Length: 122 amino acids
Theoretical weight: 14.13 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05633 (Residues: 1-122; Coverage: 91%)
Gene names: Saci_0586, rpl24
Sequence domains:
Large ribosomal subunit protein uL29 Chain: L29P
Molecule details ›
Chain: L29P
Length: 63 amino acids
Theoretical weight: 7.38 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB47 (Residues: 2-64; Coverage: 91%)
Gene names: Saci_0590, rpl29
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL30 Chain: L30E
Molecule details ›
Chain: L30E
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P11522 (Residues: 5-98; Coverage: 90%)
Gene names: Saci_0690, rpl30e
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL30 Chain: L30P
Molecule details ›
Chain: L30P
Length: 155 amino acids
Theoretical weight: 17.82 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05642 (Residues: 1-155; Coverage: 99%)
Gene names: Saci_0576, rpl30
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein eL31 Chain: L31E
Molecule details ›
Chain: L31E
Length: 75 amino acids
Theoretical weight: 8.94 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P38618 (Residues: 42-116; Coverage: 58%)
Gene names: Saci_1466, rpl31e
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: L32E
Molecule details ›
Chain: L32E
Length: 123 amino acids
Theoretical weight: 14.33 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05638 (Residues: 3-125; Coverage: 98%)
Gene names: Saci_0580, rpl32e
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL34 Chain: L34E
Molecule details ›
Chain: L34E
Length: 77 amino acids
Theoretical weight: 8.99 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05981 (Residues: 3-79; Coverage: 89%)
Gene names: Saci_0571, rl34, rpl34e
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein eL43 Chain: L37A
Molecule details ›
Chain: L37A
Length: 65 amino acids
Theoretical weight: 7.54 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB29 (Residues: 5-69; Coverage: 93%)
Gene names: Saci_0608, rpl37ae
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL37 Chain: L37E
Molecule details ›
Chain: L37E
Length: 54 amino acids
Theoretical weight: 6.27 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAZ9 (Residues: 1-54; Coverage: 89%)
Gene names: Saci_0642, rpl37e
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL39 Chain: L39E
Molecule details ›
Chain: L39E
Length: 49 amino acids
Theoretical weight: 5.86 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: P13005 (Residues: 3-51; Coverage: 96%)
Gene names: Saci_1467, rl46, rpl39e, rpl46
Sequence domains: Ribosomal L39 protein
50S ribosomal protein L40e Chain: L40E
Molecule details ›
Chain: L40E
Length: 55 amino acids
Theoretical weight: 6.34 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JAP0 (Residues: 1-55; Coverage: 98%)
Gene name: Saci_0766
Sequence domains: Ribosomal L40e family
Large ribosomal subunit protein eL42 Chain: L44E
Molecule details ›
Chain: L44E
Length: 92 amino acids
Theoretical weight: 10.81 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4J9B2 (Residues: 1-92; Coverage: 97%)
Gene names: Saci_1277, rpl44e
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL8 Chains: L7A1, L7A2
Molecule details ›
Chains: L7A1, L7A2
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
Large ribosomal subunit protein uL15 Chain: L15P
Molecule details ›
Chain: L15P
Length: 144 amino acids
Theoretical weight: 16.48 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: O05643 (Residues: 1-144; Coverage: 100%)
Gene names: Saci_0575, rpl15
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL21 Chain: L21E
Molecule details ›
Chain: L21E
Length: 97 amino acids
Theoretical weight: 11.16 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4JB11 (Residues: 2-98; Coverage: 94%)
Gene names: Saci_0626, rpl21e
Sequence domains: Ribosomal protein L21e
DUF2280 domain-containing protein Chain: L45A
Molecule details ›
Chain: L45A
Length: 101 amino acids
Theoretical weight: 11.66 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4J9G6 (Residues: 1-101; Coverage: 81%)
Gene name: Saci_1218
DUF5622 domain-containing protein Chain: L46A
Molecule details ›
Chain: L46A
Length: 70 amino acids
Theoretical weight: 8.32 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: Q4J953 (Residues: 1-70; Coverage: 93%)
Gene name: Saci_1337
Sequence domains: Domain of unknown function (DUF5622)
50S ribosomal protein L47A Chain: L47A
Molecule details ›
Chain: L47A
Length: 80 amino acids
Theoretical weight: 9.28 KDa
Source organism: Sulfolobus acidocaldarius DSM 639
UniProt:
  • Canonical: F2Z6C4 (Residues: 1-80; Coverage: 100%)
Gene name: Saci_1586
23s rRNA (2996-MER) Chain: A23S
Molecule details ›
Chain: A23S
Length: 3022 nucleotides
Theoretical weight: 980.55 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
5s rRNA (122-MER) Chain: A5S
Molecule details ›
Chain: A5S
Length: 122 nucleotides
Theoretical weight: 39.44 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.94Å
Relevant EMDB volumes: EMD-34861

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