› 8rjd

Electron Microscopy
2.79Å resolution

Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2

Released:
DOI: 10.2210/pdb8rjd/pdb
PDB entry 8rjd coloured by chain, front view.
PDB entry 8rjd coloured by chain, side view.
PDB entry 8rjd coloured by chain, top view.
Source organisms:
Primary publication:
Structural analysis of the dynamic ribosome-translocon complex.
Lewis AJO, Zhong F, Keenan RJ, Hegde RS
Elife 13 (2024)
PMID: 38896445
Related structures: EMD-19198

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
PDBe Complex ID:
PDB-CPX-275610 (preferred)
Entry contents:
52 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (56 distinct):
Protein transport protein Sec61 subunit alpha isoform 1 Chain: 1
Molecule details ›
Chain: 1
Length: 476 amino acids
Theoretical weight: 52.28 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P38377 (Residues: 1-476; Coverage: 100%)
Gene name: SEC61A1
Sequence domains:
Protein transport protein Sec61 subunit beta Chain: 2
Molecule details ›
Chain: 2
Length: 96 amino acids
Theoretical weight: 9.99 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P60467 (Residues: 1-96; Coverage: 100%)
Gene name: SEC61B
Sequence domains: Sec61beta family
Protein transport protein Sec61 subunit gamma Chain: 3
Molecule details ›
Chain: 3
Length: 68 amino acids
Theoretical weight: 7.75 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P60058 (Residues: 1-68; Coverage: 100%)
Gene name: SEC61G
Sequence domains: SecE/Sec61-gamma subunits of protein translocation complex
Stress-associated endoplasmic reticulum protein Chain: 4
Molecule details ›
Chain: 4
Length: 66 amino acids
Theoretical weight: 7.38 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: A0A8I3PRN4 (Residues: 1-66; Coverage: 100%)
Gene name: SERP1
Sequence domains: Ribosome associated membrane protein RAMP4
Translocon-associated protein subunit alpha Chain: 5
Molecule details ›
Chain: 5
Length: 286 amino acids
Theoretical weight: 32 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P16967 (Residues: 1-286; Coverage: 100%)
Gene name: SSR1
Sequence domains: Translocon-associated protein (TRAP), alpha subunit
Translocon-associated protein subunit beta Chain: 6
Molecule details ›
Chain: 6
Length: 183 amino acids
Theoretical weight: 20.12 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P23438 (Residues: 1-183; Coverage: 100%)
Gene name: SSR2
Sequence domains: Translocon-associated protein beta (TRAPB)
Translocon-associated protein subunit gamma Chain: 7
Molecule details ›
Chain: 7
Length: 185 amino acids
Theoretical weight: 21.09 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: A0A8C0T6I4 (Residues: 1-185; Coverage: 100%)
Gene name: SSR3
Sequence domains: Translocon-associated protein, gamma subunit (TRAP-gamma)
Translocon-associated protein subunit delta Chain: 8
Molecule details ›
Chain: 8
Length: 173 amino acids
Theoretical weight: 18.96 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: A0A8I3PXW2 (Residues: 1-173; Coverage: 100%)
Gene name: SSR4
Sequence domains: Translocon-associated protein, delta subunit precursor (TRAP-delta)
Calnexin Chain: 9
Molecule details ›
Chain: 9
Length: 593 amino acids
Theoretical weight: 67.69 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P24643 (Residues: 1-593; Coverage: 100%)
Gene name: CANX
Sequence domains: Calreticulin family
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TT27 (Residues: 1-257; Coverage: 100%)
Gene name: RPL8
Sequence domains:
Rhodopsin Chain: B
Molecule details ›
Chain: B
Length: 229 amino acids
Theoretical weight: 23.49 KDa
Source organism: Bos taurus
Expression system: Oryctolagus cuniculus
UniProt:
  • Canonical: P02699 (Residues: 32-109; Coverage: 22%)
Gene name: RHO
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 425 amino acids
Theoretical weight: 47.73 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVW5 (Residues: 1-378, 379-413; Coverage: 100%)
Gene name: RPL4
Sequence domains:
Large ribosomal subunit protein uL18 Chain: D
Molecule details ›
Chain: D
Length: 297 amino acids
Theoretical weight: 34.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: P19949 (Residues: 1-297; Coverage: 100%)
Gene name: RPL5
Large ribosomal subunit protein eL6 Chain: E
Molecule details ›
Chain: E
Length: 291 amino acids
Theoretical weight: 33.03 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SKF7 (Residues: 1-291; Coverage: 100%)
Gene name: RPL6
Sequence domains:
Large ribosomal subunit protein uL30 Chain: F
Molecule details ›
Chain: F
Length: 247 amino acids
Theoretical weight: 29.2 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SV32 (Residues: 1-208; Coverage: 100%)
Gene name: RPL7
Sequence domains:
Large ribosomal subunit protein eL8 Chain: G
Molecule details ›
Chain: G
Length: 319 amino acids
Theoretical weight: 36.22 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1STW0 (Residues: 1-319; Coverage: 100%)
Gene name: RPL7A
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: 21.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SWI6 (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: 214 amino acids
Theoretical weight: 24.64 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B7NZQ2 (Residues: 1-214; Coverage: 100%)
Gene name: RPL10
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein uL5 Chain: J
Molecule details ›
Chain: J
Length: 178 amino acids
Theoretical weight: 20.29 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUB8 (Residues: 1-178; Coverage: 100%)
Gene name: RPL11
Sequence domains:
Large ribosomal subunit protein eL13 Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 24.33 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TKB3 (Residues: 32-32, 34-65, 68-69, 74-74, 76-79, 82-91, 94-129; Coverage: 41%)
Gene name: RPL13
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14 Chain: M
Molecule details ›
Chain: M
Length: 218 amino acids
Theoretical weight: 23.87 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ12 (Residues: 1-218; Coverage: 100%)
Gene name: RPL14
Sequence domains: Ribosomal protein L14
Large ribosomal subunit protein eL15 Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T0C1 (Residues: 1-204; Coverage: 100%)
Gene name: RPL15
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13 Chain: O
Molecule details ›
Chain: O
Length: 203 amino acids
Theoretical weight: 23.53 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TVS8 (Residues: 1-203; Coverage: 100%)
Gene name: RPL13A
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 184 amino acids
Theoretical weight: 21.44 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SCJ6 (Residues: 1-184; Coverage: 100%)
Gene name: RPL17
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18 Chain: Q
Molecule details ›
Chain: Q
Length: 187 amino acids
Theoretical weight: 21.57 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TFE0 (Residues: 2-188; Coverage: 100%)
Gene name: RPL18
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 Chain: R
Molecule details ›
Chain: R
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TYL6 (Residues: 1-196; Coverage: 100%)
Gene name: RPL19
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL20 Chain: S
Molecule details ›
Chain: S
Length: 176 amino acids
Theoretical weight: 20.83 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TTY7 (Residues: 1-176; 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: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SHQ2 (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: 14.81 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TSG1 (Residues: 1-128; Coverage: 100%)
Gene name: RPL22
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL14 Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T6D1 (Residues: 1-140; Coverage: 100%)
Gene name: RPL23
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24 Chain: W
Molecule details ›
Chain: W
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SE28 (Residues: 1-157; Coverage: 100%)
Gene name: RPL24
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 156 amino acids
Theoretical weight: 17.77 KDa
Source organism: Oryctolagus
UniProt:
  • Canonical: G1SE76 (Residues: 1-156; Coverage: 100%)
Gene name: RPL23A
Sequence domains:
Large ribosomal subunit protein uL24 Chain: Y
Molecule details ›
Chain: Y
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Oryctolagus
UniProt:
  • Canonical: G1SQH0 (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: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TXF6 (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: 16.62 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SNY0 (Residues: 1-148; Coverage: 100%)
Gene name: RPL27A
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL29 Chain: b
Molecule details ›
Chain: b
Length: 226 amino acids
Theoretical weight: 24.93 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGR6 (Residues: 1-226; Coverage: 92%)
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: Oryctolagus
UniProt:
  • Canonical: G1TDL2 (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: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SHG0 (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: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUN8 (Residues: 1-135; Coverage: 100%)
Gene name: RPL32
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33 Chain: f
Molecule details ›
Chain: f
Length: 110 amino acids
Theoretical weight: 12.58 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SF08 (Residues: 1-110; Coverage: 100%)
Gene name: RPL35A
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL34 Chain: g
Molecule details ›
Chain: g
Length: 116 amino acids
Theoretical weight: 13.2 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TXG5 (Residues: 1-116; Coverage: 99%)
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: 14.57 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIT5 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36 Chain: i
Molecule details ›
Chain: i
Length: 105 amino acids
Theoretical weight: 12.26 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TTQ5 (Residues: 1-105; Coverage: 100%)
Gene name: RPL36
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37 Chain: j
Molecule details ›
Chain: j
Length: 97 amino acids
Theoretical weight: 11.11 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: U3KPD5 (Residues: 1-97; Coverage: 100%)
Gene name: RPL37
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein eL38 Chain: k
Molecule details ›
Chain: k
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Oryctolagus
UniProt:
  • Canonical: G1U001 (Residues: 1-70; Coverage: 100%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL39 Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.46 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TTN1 (Residues: 1-51; Coverage: 100%)
Sequence domains: Ribosomal L39 protein
Ubiquitin Chain: m
Molecule details ›
Chain: m
Length: 102 amino acids
Theoretical weight: 11.7 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: P0DXC2 (Residues: 36-128; Coverage: 73%)
Gene name: UBA52
Small ribosomal subunit protein eS32 Chain: n
Molecule details ›
Chain: n
Length: 25 amino acids
Theoretical weight: 3.47 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A087WNH4 (Residues: 1-25; Coverage: 100%)
Gene name: RPL41
Sequence domains: Ribosomal protein L41
Large ribosomal subunit protein eL42 Chain: o
Molecule details ›
Chain: o
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1T040 (Residues: 1-100; Coverage: 90%)
Gene name: RPL36A
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein eL43 Chain: p
Molecule details ›
Chain: p
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SY53 (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: Oryctolagus cuniculus
UniProt:
  • Canonical: G1U7L1 (Residues: 1-137; Coverage: 100%)
Gene name: RPL28
Sequence domains: Ribosomal L28e protein family
Large ribosomal subunit protein uL3 Chain: w
Molecule details ›
Chain: w
Length: 403 amino acids
Theoretical weight: 46.11 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TL06 (Residues: 1-403; Coverage: 100%)
Gene name: RPL3
Sequence domains: Ribosomal protein L3
28S ribosomal RNA Chain: K
Molecule details ›
Chain: K
Length: 3543 nucleotides
Theoretical weight: 1148.12 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
P-site tRNA Chain: q
Molecule details ›
Chain: q
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Sequence domains: tRNA
5S ribosomal RNA Chain: u
Molecule details ›
Chain: u
Length: 120 nucleotides
Theoretical weight: 38.69 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: v
Molecule details ›
Chain: v
Length: 156 nucleotides
Theoretical weight: 50.14 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand MG 218 x MG
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.786Å
Relevant EMDB volumes: EMD-19198
Expression system: Oryctolagus cuniculus

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