› 4adx

Electron Microscopy
6.6Å resolution

The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6

Released:
DOI: 10.2210/pdb4adx/pdb
PDB entry 4adx coloured by chain, front view.
PDB entry 4adx coloured by chain, side view.
PDB entry 4adx coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Primary publication:
Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution.
Greber BJ, Boehringer D, Godinic-Mikulcic V, Crnkovic A, Ibba M, Weygand-Durasevic I, Ban N
J Mol Biol 418 145-60 (2012)
PMID: 22306461
Related structures: EMD-2012

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-127903 (preferred)
Entry contents:
33 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (36 distinct):
Large ribosomal subunit protein eL37 Chain: 1
Molecule details ›
Chain: 1
Length: 57 amino acids
Theoretical weight: 6.33 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P32410 (Residues: 1-57; Coverage: 100%)
Gene names: rpl37e, rrnAC0797.1
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL39 Chain: 2
Molecule details ›
Chain: 2
Length: 50 amino acids
Theoretical weight: 6.13 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P22452 (Residues: 1-50; Coverage: 100%)
Gene names: rpl39e, rrnAC3112
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL42 Chain: 3
Molecule details ›
Chain: 3
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P32411 (Residues: 1-92; Coverage: 100%)
Gene names: rpl44e, rrnAC3514
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL34 Chain: 4
Molecule details ›
Chain: 4
Length: 123 amino acids
Theoretical weight: 14.07 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P0DJ23 (Residues: 1-123; Coverage: 100%)
Gene name: RPL34
Sequence domains: Ribosomal protein L34e
Ubiquitin-ribosomal protein eL40 fusion protein Chain: 5
Molecule details ›
Chain: 5
Length: 129 amino acids
Theoretical weight: 14.6 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P0DJ25 (Residues: 1-129; Coverage: 100%)
Gene name: RPL40
Sequence domains:
Large ribosomal subunit protein eL30 Chain: 6
Molecule details ›
Chain: 6
Length: 104 amino acids
Theoretical weight: 11.37 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P0DJ59 (Residues: 1-104; Coverage: 100%)
Gene names: RPL30, TTHERM_00446280A
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL14 Chain: 7
Molecule details ›
Chain: 7
Length: 126 amino acids
Theoretical weight: 14.63 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: Q24C27 (Residues: 1-126; Coverage: 100%)
Gene names: RPL14, TTHERM_00697490A
Sequence domains:
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 240 amino acids
Theoretical weight: 25.35 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P20276 (Residues: 1-240; Coverage: 100%)
Gene names: rpl2, rrnAC1608
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 338 amino acids
Theoretical weight: 37.4 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P20279 (Residues: 1-338; Coverage: 100%)
Gene names: rpl3, rrnAC1611
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 246 amino acids
Theoretical weight: 26.46 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12735 (Residues: 1-246; Coverage: 100%)
Gene names: rpl4, rrnAC1610
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: D
Molecule details ›
Chain: D
Length: 177 amino acids
Theoretical weight: 19.55 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P14124 (Residues: 1-177; Coverage: 100%)
Gene names: rpl5, rrnAC1598
Sequence domains:
Large ribosomal subunit protein uL6 Chain: E
Molecule details ›
Chain: E
Length: 178 amino acids
Theoretical weight: 19.96 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P14135 (Residues: 1-178; Coverage: 100%)
Gene names: rpl6, rrnAC1596
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein eL8 Chain: F
Molecule details ›
Chain: F
Length: 120 amino acids
Theoretical weight: 12.79 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12743 (Residues: 1-120; Coverage: 100%)
Gene names: rpl7ae, rrnAC0103
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL20 Chain: G
Molecule details ›
Chain: G
Length: 78 amino acids
Theoretical weight: 9.3 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: O27647 (Residues: 1-78; Coverage: 100%)
Gene names: MTH_1610, rpl18a, rpl20e, rplX
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein uL16 Chain: H
Molecule details ›
Chain: H
Length: 177 amino acids
Theoretical weight: 19.94 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P60617 (Residues: 1-177; Coverage: 100%)
Gene names: rpl10e, rrnAC2357
Sequence domains: Ribosomal protein L16p/L10e
Translation initiation factor 6 Chain: I
Molecule details ›
Chain: I
Length: 222 amino acids
Theoretical weight: 22.67 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: O27648 (Residues: 1-222; Coverage: 100%)
Gene names: MTH_1611, eif6
Sequence domains: eIF-6 family
RPL13 Chain: J
Molecule details ›
Chain: J
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
Large ribosomal subunit protein uL14 Chain: K
Molecule details ›
Chain: K
Length: 132 amino acids
Theoretical weight: 14.22 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P22450 (Residues: 1-132; Coverage: 100%)
Gene names: rpl14, rrnAC1602
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: L
Molecule details ›
Chain: L
Length: 165 amino acids
Theoretical weight: 18.01 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12737 (Residues: 1-165; Coverage: 100%)
Gene names: rpl15, rrnAC1590
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL15 Chain: M
Molecule details ›
Chain: M
Length: 196 amino acids
Theoretical weight: 22.4 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P60618 (Residues: 1-196; Coverage: 100%)
Gene names: rpl15e, rrnAC2065
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL18 Chain: N
Molecule details ›
Chain: N
Length: 187 amino acids
Theoretical weight: 20.64 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P14123 (Residues: 1-187; Coverage: 100%)
Gene names: rpl18, rrnAC1593
Sequence domains: Ribosomal large subunit proteins 60S L5, and 50S L18
Large ribosomal subunit protein eL18 Chain: O
Molecule details ›
Chain: O
Length: 116 amino acids
Theoretical weight: 12.44 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12733 (Residues: 1-116; Coverage: 100%)
Gene names: rpl18e, rrnAC0064
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL19 Chain: P
Molecule details ›
Chain: P
Length: 149 amino acids
Theoretical weight: 16.8 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P14119 (Residues: 1-149; Coverage: 100%)
Gene names: rpl19e, rrnAC1594
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL21 Chain: Q
Molecule details ›
Chain: Q
Length: 96 amino acids
Theoretical weight: 10.57 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12734 (Residues: 1-96; Coverage: 100%)
Gene names: rpl21e, rrnAC0260
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein uL22 Chain: R
Molecule details ›
Chain: R
Length: 155 amino acids
Theoretical weight: 16.97 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P10970 (Residues: 1-155; Coverage: 100%)
Gene names: rpl22, rrnAC1606
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: S
Molecule details ›
Chain: S
Length: 85 amino acids
Theoretical weight: 9.61 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12732 (Residues: 1-85; Coverage: 100%)
Gene names: rpl23, rrnAC1609
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: T
Molecule details ›
Chain: T
Length: 120 amino acids
Theoretical weight: 13.67 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P10972 (Residues: 1-120; Coverage: 100%)
Gene names: rpl24, rrnAC1601
Sequence domains:
Large ribosomal subunit protein eL24 Chain: U
Molecule details ›
Chain: U
Length: 67 amino acids
Theoretical weight: 7.36 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P14116 (Residues: 1-67; Coverage: 100%)
Gene names: rpl24e, rrnAC0104
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL29 Chain: V
Molecule details ›
Chain: V
Length: 71 amino acids
Theoretical weight: 7.89 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P10971 (Residues: 1-71; Coverage: 100%)
Gene names: rpl29, rrnAC1604
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: W
Molecule details ›
Chain: W
Length: 154 amino acids
Theoretical weight: 17.06 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P14121 (Residues: 1-154; Coverage: 100%)
Gene names: rpl30, rrnAC1591
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein eL31 Chain: X
Molecule details ›
Chain: X
Length: 92 amino acids
Theoretical weight: 10.38 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P18138 (Residues: 1-92; Coverage: 100%)
Gene names: rpl31e, rrnAC3113
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: Y
Molecule details ›
Chain: Y
Length: 241 amino acids
Theoretical weight: 26.46 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P12736 (Residues: 1-241; Coverage: 100%)
Gene names: rpl32e, rrnAC1595
Sequence domains:
Large ribosomal subunit protein eL43 Chain: Z
Molecule details ›
Chain: Z
Length: 92 amino acids
Theoretical weight: 10.19 KDa
Source organism: Methanothermobacter thermautotrophicus str. Delta H
UniProt:
  • Canonical: P60619 (Residues: 1-92; Coverage: 100%)
Gene names: rpl37ae, rrnAC1669
Sequence domains: Ribosomal L37ae protein family
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2923 nucleotides
Theoretical weight: 946.41 KDa
Sequence domains: Archaeal large subunit ribosomal RNA
23S Ribosomal RNA EXPANSION SEGMENTS Chain: 8
Molecule details ›
Chain: 8
Length: 133 nucleotides
Theoretical weight: 43.05 KDa
5S ribosomal RNA Chain: 9
Molecule details ›
Chain: 9
Length: 122 nucleotides
Theoretical weight: 39.3 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 6.6Å
Relevant EMDB volumes: EMD-2012

Quick links

Citations

3 review citations

Atypical protein kinases of the RIO family in archaea.
Esser et al. (2013)
2 more

4 mentions without citation

Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs.
Godinic-Mikulcic et al. (2014)
3 more