› 3j7q

Electron Microscopy
3.5Å resolution

Structure of the idle mammalian ribosome-Sec61 complex

Released:
DOI: 10.2210/pdb3j7q/pdb
PDB entry 3j7q coloured by chain, front view.
PDB entry 3j7q coloured by chain, side view.
PDB entry 3j7q coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution.
Voorhees RM, Fernández IS, Scheres SH, Hegde RS
Cell 157 1632-43 (2014)
PMID: 24930395
Related structures: EMD-2650

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 48-mer (preferred)
PDBe Complex ID:
PDB-CPX-236684 (preferred)
Entry contents:
45 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (48 distinct):
Ribosomal protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Sus scrofa
Ribosomal protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 394 amino acids
Theoretical weight: 44.76 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 367 amino acids
Theoretical weight: 41.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SJJ5 (Residues: 2-353, 354-365; Coverage: 85%)
Gene name: RPL4
Sequence domains:
Large ribosomal subunit protein uL18 Chain: D
Molecule details ›
Chain: D
Length: 297 amino acids
Theoretical weight: 34.42 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ASD0 (Residues: 1-297; Coverage: 100%)
Gene name: RPL5
Sequence domains:
Large ribosomal subunit protein eL6 Chain: E
Molecule details ›
Chain: E
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2YGT9 (Residues: 38-284; Coverage: 83%)
Gene name: RPL6
Sequence domains:
Ribosomal protein uL30 Chain: F
Molecule details ›
Chain: F
Length: 225 amino acids
Theoretical weight: 26.59 KDa
Source organism: Sus scrofa
60S ribosomal protein L7a Chain: G
Molecule details ›
Chain: G
Length: 266 amino acids
Theoretical weight: 30.17 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1W808 (Residues: 35-300; Coverage: 89%)
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6 Chain: H
Molecule details ›
Chain: H
Length: 192 amino acids
Theoretical weight: 21.9 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LP78 (Residues: 1-192; Coverage: 100%)
Gene name: RPL9
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL16 Chain: I
Molecule details ›
Chain: I
Length: 213 amino acids
Theoretical weight: 24.47 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q29195 (Residues: 2-214; Coverage: 100%)
Gene names: QM, RPL10
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5 Chain: J
Molecule details ›
Chain: J
Length: 178 amino acids
Theoretical weight: 20.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q29205 (Residues: 1-178; Coverage: 100%)
Gene name: RPL11
Sequence domains:
60S ribosomal protein L13 Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 24.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TBV3 (Residues: 218-428; Coverage: 49%)
Gene name: RPL13
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 Chain: M
Molecule details ›
Chain: M
Length: 213 amino acids
Theoretical weight: 23.38 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A1XQU3 (Residues: 1-213; Coverage: 100%)
Gene name: RPL14
Sequence domains: Ribosomal protein L14
Ribosomal protein L15 Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZL65 (Residues: 1-204; Coverage: 100%)
Gene name: RPL15
Sequence domains: Ribosomal L15
Ribosomal protein uL13 Chain: O
Molecule details ›
Chain: O
Length: 201 amino acids
Theoretical weight: 23.44 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 153 amino acids
Theoretical weight: 17.76 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287B386 (Residues: 2-154; Coverage: 82%)
Gene name: RPL17
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: Q
Molecule details ›
Chain: Q
Length: 188 amino acids
Theoretical weight: 21.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1W0N5 (Residues: 1-188; Coverage: 100%)
Gene name: RPL18
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Ribosomal protein eL19 Chain: R
Molecule details ›
Chain: R
Length: 196 amino acids
Theoretical weight: 23.57 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein eL20 Chain: S
Molecule details ›
Chain: S
Length: 224 amino acids
Theoretical weight: 26.1 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287APR1 (Residues: 1-224; Coverage: 100%)
Gene name: RPL18A
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21 Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P49666 (Residues: 1-160; Coverage: 100%)
Gene name: RPL21
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22 Chain: U
Molecule details ›
Chain: U
Length: 128 amino acids
Theoretical weight: 14.78 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P67985 (Residues: 1-128; Coverage: 100%)
Gene name: RPL22
Sequence domains: Ribosomal L22e protein family
Ribosomal protein uL14 Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein eL24 Chain: W
Molecule details ›
Chain: W
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SH42 (Residues: 1-157; Coverage: 100%)
Gene name: RPL24
Sequence domains: Ribosomal protein L24e
Ribosomal protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein uL24 Chain: Y
Molecule details ›
Chain: Y
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1V977 (Residues: 1-145; Coverage: 100%)
Gene name: RPL26
Sequence domains:
Large ribosomal subunit protein eL27 Chain: Z
Molecule details ›
Chain: Z
Length: 136 amino acids
Theoretical weight: 15.84 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A1XQU5 (Residues: 1-136; Coverage: 100%)
Gene name: RPL27
Sequence domains:
Large ribosomal subunit protein uL15 Chain: a
Molecule details ›
Chain: a
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1SN08 (Residues: 116-263; Coverage: 56%)
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL29 Chain: b
Molecule details ›
Chain: b
Length: 160 amino acids
Theoretical weight: 17.55 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q95281 (Residues: 1-160; Coverage: 100%)
Gene name: RPL29
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein eL30 Chain: c
Molecule details ›
Chain: c
Length: 115 amino acids
Theoretical weight: 12.81 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TXJ8 (Residues: 1-115; Coverage: 100%)
Gene name: RPL30
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL31 Chain: d
Molecule details ›
Chain: d
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P62901 (Residues: 1-125; Coverage: 100%)
Gene name: RPL31
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: e
Molecule details ›
Chain: e
Length: 135 amino acids
Theoretical weight: 15.9 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q6QAT0 (Residues: 1-135; Coverage: 100%)
Gene name: RPL32
Sequence domains: Ribosomal protein L32
Ribosomal protein eL33 Chain: f
Molecule details ›
Chain: f
Length: 110 amino acids
Theoretical weight: 12.56 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein eL34 Chain: g
Molecule details ›
Chain: g
Length: 117 amino acids
Theoretical weight: 13.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q29223 (Residues: 1-117; Coverage: 100%)
Gene name: RPL34
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29 Chain: h
Molecule details ›
Chain: h
Length: 123 amino acids
Theoretical weight: 14.59 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q29361 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
Ribosomal protein eL36 Chain: i
Molecule details ›
Chain: i
Length: 105 amino acids
Theoretical weight: 12.29 KDa
Source organism: Sus scrofa
Ribosomal protein eL37 Chain: j
Molecule details ›
Chain: j
Length: 86 amino acids
Theoretical weight: 10.1 KDa
Source organism: Sus scrofa
Large ribosomal subunit protein eL38 Chain: k
Molecule details ›
Chain: k
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VLH7 (Residues: 1-70; Coverage: 100%)
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.43 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GP63 (Residues: 1-51; Coverage: 100%)
Gene names: LOC100525679, LOC100623540, RPL39
Sequence domains: Ribosomal L39 protein
Ubiquitin-ribosomal protein eL40 fusion protein Chain: m
Molecule details ›
Chain: m
Length: 128 amino acids
Theoretical weight: 14.76 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P63053 (Residues: 1-128; Coverage: 100%)
Gene names: UBA52, UBCEP2
Sequence domains:
Ribosomal protein eL41 Chain: n
Molecule details ›
Chain: n
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Sus scrofa
Ribosomal protein eL42 Chain: o
Molecule details ›
Chain: o
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Sus scrofa
Ribosomal protein eL43 Chain: p
Molecule details ›
Chain: p
Length: 91 amino acids
Theoretical weight: 10.17 KDa
Source organism: Sus scrofa
Ribosomal protein eL28 Chain: r
Molecule details ›
Chain: r
Length: 125 amino acids
Theoretical weight: 14.3 KDa
Source organism: Sus scrofa
Sec61 alpha subunit Chain: 1
Molecule details ›
Chain: 1
Length: 476 amino acids
Theoretical weight: 52.28 KDa
Source organism: Sus scrofa
Sec61 gamma subunit Chain: 2
Molecule details ›
Chain: 2
Length: 68 amino acids
Theoretical weight: 7.75 KDa
Source organism: Sus scrofa
Sec61 beta subunit Chain: 3
Molecule details ›
Chain: 3
Length: 36 amino acids
Theoretical weight: 3.08 KDa
Source organism: Sus scrofa
28S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 3722 nucleotides
Theoretical weight: 1206.1 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 7
Molecule details ›
Chain: 7
Length: 120 nucleotides
Theoretical weight: 38.69 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 8
Molecule details ›
Chain: 8
Length: 156 nucleotides
Theoretical weight: 50.14 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 130 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-2650

Quick links

Citations

53 review citations

Mechanisms of integral membrane protein insertion and folding.
Cymer et al. (2015)
52 more

24 mentions without citation

Complexity and Specificity of Sec61-Channelopathies: Human Diseases Affecting Gating of the Sec61 Complex.
Sicking et al. (2021)
23 more