› 7nfx

Electron Microscopy
3.2Å resolution

Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A

Released:
DOI: 10.2210/pdb7nfx/pdb
PDB entry 7nfx coloured by chain, front view.
PDB entry 7nfx coloured by chain, side view.
PDB entry 7nfx coloured by chain, top view.
Source organisms:
Primary publication:
Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER.
Lee JH, Jomaa A, Chung S, Hwang Fu YH, Qian R, Sun X, Hsieh HH, Chandrasekar S, Bi X, Mattei S, Boehringer D, Weiss S, Ban N, Shan SO
OpenAccess logo Sci Adv 7 (2021)
PMID: 34020957
Related structures: EMD-12303

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-492702 (preferred)
Entry contents:
51 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (55 distinct):
uL2 Chain: A
Molecule details ›
Chain: A
Length: 245 amino acids
Theoretical weight: 26.7 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
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
Large ribosomal subunit protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 413 amino acids
Theoretical weight: 46.39 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SVW5 (Residues: 1-413; 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: 33.06 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: 225 amino acids
Theoretical weight: 26.66 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: 36.27 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:
60S ribosomal protein L13 Chain: L
Molecule details ›
Chain: L
Length: 210 amino acids
Theoretical weight: 24.22 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL14 Chain: M
Molecule details ›
Chain: M
Length: 218 amino acids
Theoretical weight: 23.81 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SZ12 (Residues: 2-218; 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
uL13 Chain: O
Molecule details ›
Chain: O
Length: 199 amino acids
Theoretical weight: 23.25 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 153 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SCJ6 (Residues: 2-154; Coverage: 83%)
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: 187 amino acids
Theoretical weight: 21.46 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TX70 (Residues: 8-194; Coverage: 96%)
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL19 Chain: R
Molecule details ›
Chain: R
Length: 180 amino acids
Theoretical weight: 21.61 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: Q3T0W9 (Residues: 2-181; Coverage: 92%)
Gene name: RPL19
Sequence domains: Ribosomal protein L19e
eL20 Chain: S
Molecule details ›
Chain: S
Length: 175 amino acids
Theoretical weight: 20.7 KDa
Source organism: Oryctolagus cuniculus
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: 99 amino acids
Theoretical weight: 11.48 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TSG1 (Residues: 17-115; Coverage: 77%)
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: 63 amino acids
Theoretical weight: 7.51 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SE28 (Residues: 1-63; Coverage: 40%)
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 cuniculus
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 cuniculus
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: 223 amino acids
Theoretical weight: 24.61 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SGR6 (Residues: 1-225; Coverage: 88%)
Gene name: RPL29
Sequence domains: Ribosomal L29e protein family
eL30 Chain: c
Molecule details ›
Chain: c
Length: 94 amino acids
Theoretical weight: 10.5 KDa
Source organism: Oryctolagus cuniculus
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: 128 amino acids
Theoretical weight: 15.02 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TUN8 (Residues: 2-129; Coverage: 95%)
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: 129 amino acids
Theoretical weight: 14.56 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TXG5 (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: 14.57 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SIT5 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
eL36 Chain: i
Molecule details ›
Chain: i
Length: 104 amino acids
Theoretical weight: 12.13 KDa
Source organism: Oryctolagus cuniculus
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
eL38 Chain: k
Molecule details ›
Chain: k
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Oryctolagus cuniculus
Large ribosomal subunit protein eL39 Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.43 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1SYU7 (Residues: 1-51; Coverage: 100%)
Gene name: RPL39
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL40 Chain: m
Molecule details ›
Chain: m
Length: 52 amino acids
Theoretical weight: 6.2 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: P63048 (Residues: 77-128; Coverage: 41%)
Gene names: UBA52, UBCEP2
Sequence domains: Ribosomal L40e family
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: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5F9D391 (Residues: 36-140; Coverage: 75%)
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
Signal recognition particle 19 kDa protein Chain: q
Molecule details ›
Chain: q
Length: 144 amino acids
Theoretical weight: 16.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09132 (Residues: 1-144; Coverage: 100%)
Gene name: SRP19
Sequence domains: SRP19 protein
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
Signal Sequence Chain: s
Molecule details ›
Chain: s
Length: 21 amino acids
Theoretical weight: 1.81 KDa
Source organism: Homo sapiens
Expression system: Oryctolagus cuniculus
Signal recognition particle 14 kDa protein Chain: t
Molecule details ›
Chain: t
Length: 136 amino acids
Theoretical weight: 14.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P37108 (Residues: 1-136; Coverage: 100%)
Gene name: SRP14
Sequence domains: Signal recognition particle 14kD protein
Signal recognition particle subunit SRP68 Chain: u
Molecule details ›
Chain: u
Length: 627 amino acids
Theoretical weight: 70.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UHB9 (Residues: 1-627; Coverage: 100%)
Gene name: SRP68
Sequence domains: RNA-binding signal recognition particle 68
Signal recognition particle receptor subunit beta Chain: v
Molecule details ›
Chain: v
Length: 271 amino acids
Theoretical weight: 29.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y5M8 (Residues: 1-271; Coverage: 100%)
Gene names: PSEC0230, SRPRB
Sequence domains: Signal recognition particle receptor beta subunit
Signal recognition particle 9 kDa protein Chain: w
Molecule details ›
Chain: w
Length: 86 amino acids
Theoretical weight: 10.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49458 (Residues: 1-86; Coverage: 100%)
Gene name: SRP9
Sequence domains: Signal recognition particle 9 kDa protein (SRP9)
Signal recognition particle subunit SRP54 Chain: x
Molecule details ›
Chain: x
Length: 504 amino acids
Theoretical weight: 55.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61011 (Residues: 1-504; Coverage: 100%)
Gene name: SRP54
Sequence domains:
Signal recognition particle receptor subunit alpha Chain: y
Molecule details ›
Chain: y
Length: 638 amino acids
Theoretical weight: 69.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P08240 (Residues: 1-638; Coverage: 100%)
Gene names: SRPR, SRPRA
Sequence domains:
Signal recognition particle subunit SRP72 Chain: z
Molecule details ›
Chain: z
Length: 671 amino acids
Theoretical weight: 74.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O76094 (Residues: 1-671; Coverage: 100%)
Gene name: SRP72
Sequence domains:
SRP RNA 7SL Chain: 1
Molecule details ›
Chain: 1
Length: 299 nucleotides
Theoretical weight: 96.83 KDa
Sequence domains: Metazoan signal recognition particle RNA
28S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 3493 nucleotides
Theoretical weight: 1131.54 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

4 bound ligands:
Ligand ZN 5 x ZN
Ligand MG 2 x MG
Ligand GTP 1 x GTP
Ligand GNP 1 x GNP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-12303
Expression systems:
  • Escherichia coli
  • Oryctolagus cuniculus

Quick links

Citations

3 review citations

Targeting of Proteins for Translocation at the Endoplasmic Reticulum.
Pool MR. (2022)
2 more

2 mentions without citation

Fidelity of Cotranslational Protein Targeting to the Endoplasmic Reticulum.
Hsieh et al. (2021)
1 more