› 6frk

Electron Microscopy
3.7Å resolution

Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex

Released:
DOI: 10.2210/pdb6frk/pdb
PDB entry 6frk coloured by chain, front view.
PDB entry 6frk coloured by chain, side view.
PDB entry 6frk coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a prehandover mammalian ribosomal SRP���SRP receptor targeting complex.
Kobayashi K, Jomaa A, Lee JH, Chandrasekar S, Boehringer D, Shan SO, Ban N
Science (2018)
PMID: 29567807
Related structures: EMD-4300

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 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-124211 (preferred)
Entry contents:
53 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (58 distinct):
Ribosomal protein eL28 Chain: 3
Molecule details ›
Chain: 3
Length: 125 amino acids
Theoretical weight: 14.3 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein L12 Chain: 4
Molecule details ›
Chain: 4
Length: 163 amino acids
Theoretical weight: 17.69 KDa
Source organism: Oryctolagus cuniculus
60S acidic ribosomal protein P0 Chain: 6
Molecule details ›
Chain: 6
Length: 202 amino acids
Theoretical weight: 22.22 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein L8 Chain: A
Molecule details ›
Chain: A
Length: 244 amino acids
Theoretical weight: 26.57 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 394 amino acids
Theoretical weight: 44.76 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL4 Chain: C
Molecule details ›
Chain: C
Length: 367 amino acids
Theoretical weight: 41.64 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL18 Chain: D
Molecule details ›
Chain: D
Length: 292 amino acids
Theoretical weight: 33.94 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL6 Chain: E
Molecule details ›
Chain: E
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL30 Chain: F
Molecule details ›
Chain: F
Length: 225 amino acids
Theoretical weight: 26.59 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL8 Chain: G
Molecule details ›
Chain: G
Length: 238 amino acids
Theoretical weight: 27.26 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL6 Chain: H
Molecule details ›
Chain: H
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL16 Chain: I
Molecule details ›
Chain: I
Length: 213 amino acids
Theoretical weight: 24.47 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL5 Chain: J
Molecule details ›
Chain: J
Length: 170 amino acids
Theoretical weight: 19.36 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL13 Chain: L
Molecule details ›
Chain: L
Length: 210 amino acids
Theoretical weight: 24.23 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL14 Chain: M
Molecule details ›
Chain: M
Length: 138 amino acids
Theoretical weight: 16.13 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein L15 Chain: N
Molecule details ›
Chain: N
Length: 203 amino acids
Theoretical weight: 24.08 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL13 Chain: O
Molecule details ›
Chain: O
Length: 201 amino acids
Theoretical weight: 23.44 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL22 Chain: P
Molecule details ›
Chain: P
Length: 153 amino acids
Theoretical weight: 17.76 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL18 Chain: Q
Molecule details ›
Chain: Q
Length: 187 amino acids
Theoretical weight: 21.46 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL19 Chain: R
Molecule details ›
Chain: R
Length: 180 amino acids
Theoretical weight: 21.61 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL20 Chain: S
Molecule details ›
Chain: S
Length: 175 amino acids
Theoretical weight: 20.7 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL21 Chain: T
Molecule details ›
Chain: T
Length: 159 amino acids
Theoretical weight: 18.48 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL22 Chain: U
Molecule details ›
Chain: U
Length: 99 amino acids
Theoretical weight: 11.48 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein L23 Chain: V
Molecule details ›
Chain: V
Length: 131 amino acids
Theoretical weight: 13.97 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL24 Chain: W
Molecule details ›
Chain: W
Length: 63 amino acids
Theoretical weight: 7.51 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 119 amino acids
Theoretical weight: 13.86 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL24 Chain: Y
Molecule details ›
Chain: Y
Length: 134 amino acids
Theoretical weight: 15.89 KDa
Source organism: Oryctolagus cuniculus
60S ribosomal protein L27 Chain: Z
Molecule details ›
Chain: Z
Length: 135 amino acids
Theoretical weight: 15.7 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL15 Chain: a
Molecule details ›
Chain: a
Length: 147 amino acids
Theoretical weight: 16.5 KDa
Source organism: Oryctolagus cuniculus
60S ribosomal protein L29 Chain: b
Molecule details ›
Chain: b
Length: 75 amino acids
Theoretical weight: 8.72 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL30 Chain: c
Molecule details ›
Chain: c
Length: 94 amino acids
Theoretical weight: 10.5 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL31 Chain: d
Molecule details ›
Chain: d
Length: 107 amino acids
Theoretical weight: 12.64 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL32 Chain: e
Molecule details ›
Chain: e
Length: 128 amino acids
Theoretical weight: 15.02 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL33 Chain: f
Molecule details ›
Chain: f
Length: 109 amino acids
Theoretical weight: 12.43 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL34 Chain: g
Molecule details ›
Chain: g
Length: 114 amino acids
Theoretical weight: 12.99 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein uL29 Chain: h
Molecule details ›
Chain: h
Length: 122 amino acids
Theoretical weight: 14.46 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL36 Chain: i
Molecule details ›
Chain: i
Length: 102 amino acids
Theoretical weight: 11.92 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein L37 Chain: j
Molecule details ›
Chain: j
Length: 86 amino acids
Theoretical weight: 10.1 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL38 Chain: k
Molecule details ›
Chain: k
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL39 Chain: l
Molecule details ›
Chain: l
Length: 50 amino acids
Theoretical weight: 6.3 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL40 Chain: m
Molecule details ›
Chain: m
Length: 52 amino acids
Theoretical weight: 6.2 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL41 Chain: n
Molecule details ›
Chain: n
Length: 23 amino acids
Theoretical weight: 3.21 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL42 Chain: o
Molecule details ›
Chain: o
Length: 104 amino acids
Theoretical weight: 12.2 KDa
Source organism: Oryctolagus cuniculus
Ribosomal protein eL43 Chain: p
Molecule details ›
Chain: p
Length: 91 amino acids
Theoretical weight: 10.17 KDa
Source organism: Oryctolagus cuniculus
Signal recognition particle 19 kDa protein Chain: q
Molecule details ›
Chain: q
Length: 105 amino acids
Theoretical weight: 12.16 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: J9PAS6 (Residues: 13-117; Coverage: 73%)
Gene name: SRP19
Sequence domains: SRP19 protein
Signal recognition particle subunit SRP72 Chain: r
Molecule details ›
Chain: r
Length: 605 amino acids
Theoretical weight: 67.31 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P33731 (Residues: 1-581; Coverage: 87%)
Gene name: SRP72
Sequence domains:
Signal sequence Chain: t
Molecule details ›
Chain: t
Length: 11 amino acids
Theoretical weight: 1.26 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Oryctolagus cuniculus
Signal recognition particle subunit SRP68 Chain: u
Molecule details ›
Chain: u
Length: 568 amino acids
Theoretical weight: 65.57 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: Q00004 (Residues: 55-622; Coverage: 91%)
Gene name: SRP68
Sequence domains: RNA-binding signal recognition particle 68
Signal recognition particle receptor subunit beta Chain: v
Molecule details ›
Chain: v
Length: 213 amino acids
Theoretical weight: 23.59 KDa
Source organism: Oryctolagus cuniculus
Expression system: Escherichia coli
UniProt:
  • Canonical: G1STG2 (Residues: 60-271; Coverage: 78%)
Gene name: SRPRB
Sequence domains: Signal recognition particle receptor beta subunit
Signal recognition particle 9 kDa protein Chain: w
Molecule details ›
Chain: w
Length: 74 amino acids
Theoretical weight: 8.69 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P21262 (Residues: 2-75; Coverage: 86%)
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: 55.78 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P61010 (Residues: 1-504; Coverage: 100%)
Gene name: SRP54
Sequence domains:
SRP54-type proteins GTP-binding domain-containing protein Chain: y
Molecule details ›
Chain: y
Length: 657 amino acids
Theoretical weight: 72.23 KDa
Source organism: Oryctolagus cuniculus
Expression system: Escherichia coli
UniProt:
  • Canonical: G1TCX6 (Residues: 1-40, 41-86, 87-632; Coverage: 100%)
Gene name: SRPRA
Sequence domains:
Signal recognition particle 14 kDa protein Chain: z
Molecule details ›
Chain: z
Length: 110 amino acids
Theoretical weight: 12.51 KDa
Source organism: Canis lupus familiaris
UniProt:
  • Canonical: P16255 (Residues: 1-110; Coverage: 100%)
Gene name: SRP14
Sequence domains: Signal recognition particle 14kD protein
Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA Chain: 1
Molecule details ›
Chain: 1
Length: 299 nucleotides
Theoretical weight: 96.83 KDa
Sequence domains: Metazoan signal recognition particle RNA
tRNA Chain: 2
Molecule details ›
Chain: 2
Length: 76 nucleotides
Theoretical weight: 24.44 KDa
Sequence domains: tRNA
28S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 3658 nucleotides
Theoretical weight: 1185.36 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 MG 133 x MG
Ligand ZN 3 x ZN
Ligand GTP 1 x GTP
Ligand GNP 2 x GNP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-4300
Expression systems:
  • Oryctolagus cuniculus
  • Escherichia coli

Quick links

Citations

7 review citations

The mechanisms of integral membrane protein biogenesis.
Hegde et al. (2022)
6 more

8 mentions without citation

Noncanonical Functions and Cellular Dynamics of the Mammalian Signal Recognition Particle Components.
Faoro et al. (2021)
7 more