› 5nco

Electron Microscopy
4.8Å resolution

Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome

Released:
DOI: 10.2210/pdb5nco/pdb
PDB entry 5nco coloured by chain, front view.
PDB entry 5nco coloured by chain, side view.
PDB entry 5nco coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome.
Jomaa A, Fu YH, Boehringer D, Leibundgut M, Shan SO, Ban N
OpenAccess logo Nat Commun 8 15470 (2017)
PMID: 28524878
Related structures: EMD-3617

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 40-mer (preferred)
PDBe Complex ID:
PDB-CPX-249953 (preferred)
Entry contents:
36 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (40 distinct):
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 271 amino acids
Theoretical weight: 29.66 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 177 amino acids
Theoretical weight: 20.07 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 176 amino acids
Theoretical weight: 18.8 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL10 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 13.5 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL11 Chain: J
Molecule details ›
Chain: J
Length: 134 amino acids
Theoretical weight: 14.02 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL13 Chain: K
Molecule details ›
Chain: K
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL14 Chain: L
Molecule details ›
Chain: L
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL15 Chain: M
Molecule details ›
Chain: M
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL16 Chain: N
Molecule details ›
Chain: N
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL17 Chain: O
Molecule details ›
Chain: O
Length: 125 amino acids
Theoretical weight: 14.19 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL18 Chain: P
Molecule details ›
Chain: P
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL19 Chain: Q
Molecule details ›
Chain: Q
Length: 114 amino acids
Theoretical weight: 13.03 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL20 Chain: R
Molecule details ›
Chain: R
Length: 117 amino acids
Theoretical weight: 13.4 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL21 Chain: S
Molecule details ›
Chain: S
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL22 Chain: T
Molecule details ›
Chain: T
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL23 Chain: U
Molecule details ›
Chain: U
Length: 95 amino acids
Theoretical weight: 10.78 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL24 Chain: V
Molecule details ›
Chain: V
Length: 102 amino acids
Theoretical weight: 11.08 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL25 Chain: W
Molecule details ›
Chain: W
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL27 Chain: X
Molecule details ›
Chain: X
Length: 76 amino acids
Theoretical weight: 8.28 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL28 Chain: Y
Molecule details ›
Chain: Y
Length: 77 amino acids
Theoretical weight: 8.9 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL29 Chain: Z
Molecule details ›
Chain: Z
Length: 62 amino acids
Theoretical weight: 7.16 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein uL30 Chain: a
Molecule details ›
Chain: a
Length: 58 amino acids
Theoretical weight: 6.42 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL32 Chain: b
Molecule details ›
Chain: b
Length: 56 amino acids
Theoretical weight: 6.33 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL33 Chain: c
Molecule details ›
Chain: c
Length: 51 amino acids
Theoretical weight: 5.93 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL34 Chain: d
Molecule details ›
Chain: d
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL35 Chain: e
Molecule details ›
Chain: e
Length: 64 amino acids
Theoretical weight: 7.18 KDa
Source organism: Escherichia coli
Large ribosomal subunit protein bL36A Chain: f
Molecule details ›
Chain: f
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli
Protein translocase subunit SecY Chain: g
Molecule details ›
Chain: g
Length: 416 amino acids
Theoretical weight: 45.63 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
Protein translocase subunit SecE Chain: h
Molecule details ›
Chain: h
Length: 56 amino acids
Theoretical weight: 6.24 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
Signal recognition particle protein Chain: i
Molecule details ›
Chain: i
Length: 450 amino acids
Theoretical weight: 48.51 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
Protein-export membrane protein SecG Chain: j
Molecule details ›
Chain: j
Length: 71 amino acids
Theoretical weight: 7.23 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
Signal sequence (1A9L) Chain: k
Molecule details ›
Chain: k
Length: 23 amino acids
Theoretical weight: 2.28 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
Signal recognition particle receptor FtsY Chain: l
Molecule details ›
Chain: l
Length: 271 amino acids
Theoretical weight: 29.44 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21
4.5S SRP RNA (Ffs) Chain: 1
Molecule details ›
Chain: 1
Length: 104 nucleotides
Theoretical weight: 33.61 KDa
Source organism: Escherichia coli
Sequence domains: Bacterial small signal recognition particle RNA
P-site tRNA-CCA end Chain: 2
Molecule details ›
Chain: 2
Length: 3 nucleotides
Theoretical weight: 895 Da
Source organism: Escherichia coli
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2903 nucleotides
Theoretical weight: 941.31 KDa
Source organism: Escherichia coli
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Source organism: Escherichia coli
Sequence domains: 5S ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand ALF 2 x ALF
Ligand MG 2 x MG
Ligand GDP 2 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.8Å
Relevant EMDB volumes: EMD-3617
Expression system: Escherichia coli BL21

Quick links

Citations

10 review citations

Biochemistry and Molecular Biology of Flaviviruses.
Barrows et al. (2018)
9 more

5 mentions without citation

The Dynamic SecYEG Translocon.
Oswald et al. (2021)
4 more