› 6w6l

Electron Microscopy
3.84Å resolution

Cryo-EM structure of the human ribosome-TMCO1 translocon

Released:
DOI: 10.2210/pdb6w6l/pdb
PDB entry 6w6l coloured by chain, front view.
PDB entry 6w6l coloured by chain, side view.
PDB entry 6w6l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An ER translocon for multi-pass membrane protein biogenesis.
McGilvray PT, Anghel SA, Sundaram A, Zhong F, Trnka MJ, Fuller JR, Hu H, Burlingame AL, Keenan RJ
Elife 9 (2020)
PMID: 32820719
Related structures: EMD-21435

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 54-mer (preferred)
PDBe Complex ID:
PDB-CPX-125305 (preferred)
Entry contents:
49 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (54 distinct):
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62917 (Residues: 1-257; Coverage: 100%)
Gene name: RPL8
Sequence domains:
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 403 amino acids
Theoretical weight: 46.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P39023 (Residues: 1-403; Coverage: 100%)
Gene names: OK/SW-cl.32, RPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 427 amino acids
Theoretical weight: 47.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P36578 (Residues: 1-427; Coverage: 100%)
Gene names: RPL1, RPL4
Sequence domains:
Large ribosomal subunit protein uL18 Chain: F
Molecule details ›
Chain: F
Length: 297 amino acids
Theoretical weight: 34.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46777 (Residues: 1-297; Coverage: 100%)
Gene names: MSTP030, RPL5
Sequence domains:
Large ribosomal subunit protein eL6 Chain: G
Molecule details ›
Chain: G
Length: 288 amino acids
Theoretical weight: 32.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q02878 (Residues: 1-288; Coverage: 100%)
Gene names: RPL6, TXREB1
Sequence domains:
Large ribosomal subunit protein uL30 Chain: H
Molecule details ›
Chain: H
Length: 248 amino acids
Theoretical weight: 29.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18124 (Residues: 1-248; Coverage: 100%)
Gene name: RPL7
Sequence domains:
Large ribosomal subunit protein eL8 Chain: I
Molecule details ›
Chain: I
Length: 266 amino acids
Theoretical weight: 30.06 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62424 (Residues: 1-266; Coverage: 100%)
Gene names: RPL7A, SURF-3, SURF3
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL6 Chain: J
Molecule details ›
Chain: J
Length: 192 amino acids
Theoretical weight: 21.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P32969 (Residues: 1-192; Coverage: 100%)
Gene names: OK/SW-cl.103, RPL9, RPL9P7, RPL9P8, RPL9P9
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL16 Chain: K
Molecule details ›
Chain: K
Length: 214 amino acids
Theoretical weight: 24.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P27635 (Residues: 1-214; Coverage: 100%)
Gene names: DXS648E, QM, RPL10
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5 Chain: L
Molecule details ›
Chain: L
Length: 178 amino acids
Theoretical weight: 20.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62913 (Residues: 1-178; Coverage: 100%)
Gene name: RPL11
Sequence domains:
Large ribosomal subunit protein eL13 Chain: M
Molecule details ›
Chain: M
Length: 211 amino acids
Theoretical weight: 24.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P26373 (Residues: 1-211; Coverage: 100%)
Gene names: BBC1, OK/SW-cl.46, RPL13
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 Chain: N
Molecule details ›
Chain: N
Length: 215 amino acids
Theoretical weight: 23.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P50914 (Residues: 1-215; Coverage: 100%)
Gene name: RPL14
Sequence domains: Ribosomal protein L14
Large ribosomal subunit protein eL15 Chain: O
Molecule details ›
Chain: O
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61313 (Residues: 1-204; Coverage: 100%)
Gene names: EC45, RPL15, TCBAP0781
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13 Chain: P
Molecule details ›
Chain: P
Length: 203 amino acids
Theoretical weight: 23.63 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P40429 (Residues: 1-203; Coverage: 100%)
Gene name: RPL13A
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22 Chain: Q
Molecule details ›
Chain: Q
Length: 184 amino acids
Theoretical weight: 21.44 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18621 (Residues: 1-184; Coverage: 100%)
Gene name: RPL17
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18 Chain: R
Molecule details ›
Chain: R
Length: 188 amino acids
Theoretical weight: 21.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q07020 (Residues: 1-188; Coverage: 100%)
Gene name: RPL18
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 Chain: S
Molecule details ›
Chain: S
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P84098 (Residues: 1-196; Coverage: 100%)
Gene name: RPL19
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL20 Chain: T
Molecule details ›
Chain: T
Length: 176 amino acids
Theoretical weight: 20.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q02543 (Residues: 1-176; Coverage: 100%)
Gene name: RPL18A
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21 Chain: U
Molecule details ›
Chain: U
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46778 (Residues: 1-160; Coverage: 100%)
Gene name: RPL21
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22 Chain: V
Molecule details ›
Chain: V
Length: 128 amino acids
Theoretical weight: 14.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P35268 (Residues: 1-128; Coverage: 100%)
Gene name: RPL22
Sequence domains: Ribosomal L22e protein family
60S ribosomal protein L23 Chain: W
Molecule details ›
Chain: W
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Homo sapiens
Large ribosomal subunit protein eL24 Chain: X
Molecule details ›
Chain: X
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P83731 (Residues: 1-157; Coverage: 100%)
Gene name: RPL24
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chain: Y
Molecule details ›
Chain: Y
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62750 (Residues: 1-156; Coverage: 100%)
Gene name: RPL23A
Sequence domains:
Large ribosomal subunit protein uL24 Chain: Z
Molecule details ›
Chain: Z
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61254 (Residues: 1-145; Coverage: 100%)
Gene name: RPL26
Sequence domains:
Large ribosomal subunit protein eL27 Chain: a
Molecule details ›
Chain: a
Length: 136 amino acids
Theoretical weight: 15.84 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61353 (Residues: 1-136; Coverage: 100%)
Gene name: RPL27
Sequence domains:
Large ribosomal subunit protein uL15 Chain: b
Molecule details ›
Chain: b
Length: 148 amino acids
Theoretical weight: 16.6 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46776 (Residues: 1-148; Coverage: 100%)
Gene name: RPL27A
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL29 Chain: c
Molecule details ›
Chain: c
Length: 159 amino acids
Theoretical weight: 17.8 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P47914 (Residues: 1-159; Coverage: 100%)
Gene name: RPL29
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein eL30 Chain: d
Molecule details ›
Chain: d
Length: 115 amino acids
Theoretical weight: 12.81 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62888 (Residues: 1-115; Coverage: 100%)
Gene name: RPL30
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
60S ribosomal protein L31 Chain: e
Molecule details ›
Chain: e
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Homo sapiens
Large ribosomal subunit protein eL32 Chain: f
Molecule details ›
Chain: f
Length: 135 amino acids
Theoretical weight: 15.9 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62910 (Residues: 1-135; Coverage: 100%)
Gene names: PP9932, RPL32
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33 Chain: g
Molecule details ›
Chain: g
Length: 110 amino acids
Theoretical weight: 12.56 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P18077 (Residues: 1-110; Coverage: 100%)
Gene names: GIG33, RPL35A
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34 Chain: h
Molecule details ›
Chain: h
Length: 117 amino acids
Theoretical weight: 13.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P49207 (Residues: 1-117; Coverage: 100%)
Gene name: RPL34
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL29 Chain: i
Molecule details ›
Chain: i
Length: 123 amino acids
Theoretical weight: 14.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42766 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36 Chain: j
Molecule details ›
Chain: j
Length: 105 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9Y3U8 (Residues: 1-105; Coverage: 100%)
Gene name: RPL36
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37 Chain: k
Molecule details ›
Chain: k
Length: 97 amino acids
Theoretical weight: 11.11 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61927 (Residues: 1-97; Coverage: 100%)
Gene name: RPL37
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chain: l
Molecule details ›
Chain: l
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63173 (Residues: 1-70; Coverage: 100%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: m
Molecule details ›
Chain: m
Length: 51 amino acids
Theoretical weight: 6.43 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62891 (Residues: 1-51; Coverage: 100%)
Gene name: RPL39
Sequence domains: Ribosomal L39 protein
Small ribosomal subunit protein eS32 Chain: o
Molecule details ›
Chain: o
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62945 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Large ribosomal subunit protein eL42 Chain: p
Molecule details ›
Chain: p
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: J3KQN4 (Residues: 37-142; Coverage: 75%)
Gene name: RPL36A
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43 Chain: q
Molecule details ›
Chain: q
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61513 (Residues: 1-92; Coverage: 100%)
Gene name: RPL37A
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL28 Chain: r
Molecule details ›
Chain: r
Length: 137 amino acids
Theoretical weight: 15.78 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P46779 (Residues: 1-137; Coverage: 100%)
Gene name: RPL28
Sequence domains: Ribosomal L28e protein family
Nascent chain mixture Chain: y
Molecule details ›
Chain: y
Length: 27 amino acids
Theoretical weight: 2.32 KDa
Source organism: Homo sapiens
Protein transport protein Sec61 subunit alpha isoform 1 Chain: 1
Molecule details ›
Chain: 1
Length: 476 amino acids
Theoretical weight: 52.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61619 (Residues: 1-476; Coverage: 100%)
Gene names: SEC61A, SEC61A1
Sequence domains:
Protein transport protein Sec61 subunit gamma Chain: 2
Molecule details ›
Chain: 2
Length: 68 amino acids
Theoretical weight: 7.75 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60059 (Residues: 1-68; Coverage: 100%)
Gene name: SEC61G
Sequence domains: SecE/Sec61-gamma subunits of protein translocation complex
Protein transport protein Sec61 subunit beta Chain: 3
Molecule details ›
Chain: 3
Length: 96 amino acids
Theoretical weight: 9.99 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P60468 (Residues: 1-96; Coverage: 100%)
Gene name: SEC61B
Sequence domains: Sec61beta family
BOS complex subunit TMEM147 Chain: 4
Molecule details ›
Chain: 4
Length: 224 amino acids
Theoretical weight: 25.28 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9BVK8 (Residues: 1-224; Coverage: 100%)
Gene name: TMEM147
Sequence domains: Predicted membrane protein (DUF2053)
BOS complex subunit NCLN Chain: 5
Molecule details ›
Chain: 5
Length: 563 amino acids
Theoretical weight: 63.05 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q969V3 (Residues: 1-563; Coverage: 100%)
Gene name: NCLN
Sequence domains: Peptidase family M28
PAT complex subunit CCDC47 Chain: 7
Molecule details ›
Chain: 7
Length: 483 amino acids
Theoretical weight: 55.95 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q96A33 (Residues: 1-483; Coverage: 100%)
Gene names: CCDC47, GK001, MSTP041, PSEC0077
Sequence domains: PAT complex subunit CCDC47
Calcium load-activated calcium channel Chain: 6
Molecule details ›
Chain: 6
Length: 188 amino acids
Theoretical weight: 21.21 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q9UM00 (Residues: 52-239; Coverage: 79%)
Gene names: PNAS-10, PNAS-136, TMCC4, TMCO1, UNQ151/PRO177
Sequence domains: Integral membrane protein EMC3/TMCO1-like
5.8S ribosomal RNA Chain: D
Molecule details ›
Chain: D
Length: 157 nucleotides
Theoretical weight: 50.45 KDa
Sequence domains: 5.8S ribosomal RNA
5S ribosomal RNA Chain: E
Molecule details ›
Chain: E
Length: 119 nucleotides
Theoretical weight: 38.39 KDa
Sequence domains: 5S ribosomal RNA
28S ribosomal RNA Chain: t
Molecule details ›
Chain: t
Length: 3579 nucleotides
Theoretical weight: 1159.53 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
tRNA Chain: u
Molecule details ›
Chain: u
Length: 76 nucleotides
Theoretical weight: 24.41 KDa
Sequence domains: tRNA
tRNA Chain: v
Molecule details ›
Chain: v
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Sequence domains: tRNA

Ligands and Environments

2 bound ligands:
Ligand MG 28 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.84Å
Relevant EMDB volumes: EMD-21435

Quick links

Citations

13 review citations

Structural and molecular mechanisms for membrane protein biogenesis by the Oxa1 superfamily.
McDowell et al. (2021)
12 more

10 mentions without citation

The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum.
Tirincsi et al. (2021)
9 more