› 7qwq

Electron Microscopy
2.83Å resolution

Ternary complex of ribosome nascent chain with SRP and NAC

Released:
DOI: 10.2210/pdb7qwq/pdb
PDB entry 7qwq coloured by chain, front view.
PDB entry 7qwq coloured by chain, side view.
PDB entry 7qwq coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of signal sequence handover from NAC to SRP on ribosomes during ER-protein targeting.
Jomaa A, Gamerdinger M, Hsieh HH, Wallisch A, Chandrasekaran V, Ulusoy Z, Scaiola A, Hegde RS, Shan SO, Ban N, Deuerling E
Science 375 839-844 (2022)
PMID: 35201867
Related structures: EMD-14191

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 52-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-242944 (preferred)
Entry contents:
48 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (52 distinct):
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
Nascent chain preprolactin Chain: s
Molecule details ›
Chain: s
Length: 112 amino acids
Theoretical weight: 9.55 KDa
Source organism: Homo sapiens
Expression system: Oryctolagus cuniculus
Transcription factor BTF3 Chain: u
Molecule details ›
Chain: u
Length: 162 amino acids
Theoretical weight: 17.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P20290 (Residues: 45-206; Coverage: 79%)
Gene names: BTF3, NACB, OK/SW-cl.8
Sequence domains: NAC domain
Signal recognition particle subunit SRP68 Chain: v
Molecule details ›
Chain: v
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 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:
Large ribosomal subunit protein uL2 Chain: A
Molecule details ›
Chain: A
Length: 244 amino acids
Theoretical weight: 26.57 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TT27 (Residues: 2-245; Coverage: 95%)
Gene name: RPL8
Sequence domains:
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
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 403 amino acids
Theoretical weight: 46.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: G1TL06 (Residues: 1-403; Coverage: 100%)
Gene name: RPL3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein eL30 Chain: c
Molecule details ›
Chain: c
Length: 115 amino acids
Theoretical weight: 12.82 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TDL2 (Residues: 1-115; Coverage: 100%)
Gene name: RPL30
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
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 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 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 eL32 Chain: e
Molecule details ›
Chain: e
Length: 157 amino acids
Theoretical weight: 18.35 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 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 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 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 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 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 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 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 eL36 Chain: i
Molecule details ›
Chain: i
Length: 102 amino acids
Theoretical weight: 11.89 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: G1TTQ5 (Residues: 2-103; Coverage: 97%)
Gene name: RPL36
Sequence domains: Ribosomal protein L36e
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 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 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 eL38 Chain: k
Molecule details ›
Chain: k
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: B5FYZ2 (Residues: 2-70; Coverage: 99%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
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 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 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
Ubiquitin-ribosomal protein eL40 fusion protein Chain: m
Molecule details ›
Chain: m
Length: 128 amino acids
Theoretical weight: 14.76 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A2U3YV30 (Residues: 1-128; Coverage: 100%)
Gene name: UBA52
Sequence domains:
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
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
Fms related receptor tyrosine kinase 3 ligand Chain: O
Molecule details ›
Chain: O
Length: 500 amino acids
Theoretical weight: 56.5 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A287B929 (Residues: 68-184, 185-279; Coverage: 74%)
Gene name: FLT3LG
Sequence domains: flt3 ligand
Large ribosomal subunit protein eL42 Chain: o
Molecule details ›
Chain: o
Length: 141 amino acids
Theoretical weight: 16.13 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: A0A5F9D391 (Residues: 1-141; Coverage: 100%)
Sequence domains: Ribosomal protein L44
60S ribosomal protein L17 Chain: P
Molecule details ›
Chain: P
Length: 153 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
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
eL18 Chain: Q
Molecule details ›
Chain: Q
Length: 187 amino acids
Theoretical weight: 21.46 KDa
Source organism: Oryctolagus cuniculus
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 eL19 Chain: R
Molecule details ›
Chain: R
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Oryctolagus cuniculus
UniProt:
  • Canonical: Q3T0W9 (Residues: 1-196; Coverage: 100%)
Gene name: RPL19
Sequence domains: Ribosomal protein L19e
60S ribosomal protein L18a 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
Ribosomal protein L22 Chain: U
Molecule details ›
Chain: U
Length: 102 amino acids
Theoretical weight: 11.84 KDa
Source organism: Oryctolagus cuniculus
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 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
Nascent polypeptide-associated complex subunit alpha Chain: t
Molecule details ›
Chain: t
Length: 215 amino acids
Theoretical weight: 23.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13765 (Residues: 1-215; Coverage: 100%)
Gene names: HSD48, NACA
Sequence domains:
SRP RNA 7SL Chain: 1
Molecule details ›
Chain: 1
Length: 167 nucleotides
Theoretical weight: 54.1 KDa
Sequence domains: Metazoan signal recognition particle RNA
28S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 4754 nucleotides
Theoretical weight: 1539.03 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 97 x MG
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.83Å
Relevant EMDB volumes: EMD-14191
Expression systems:
  • Escherichia coli
  • Oryctolagus cuniculus

Quick links

Citations

8 review citations

Daylight-PDT: everything under the sun.
Beiki et al. (2022)
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