› 3ndb

X-ray diffraction
3Å resolution

Crystal structure of a signal sequence bound to the signal recognition particle

Released:
DOI: 10.2210/pdb3ndb/pdb
PDB entry 3ndb coloured by chain, front view.
PDB entry 3ndb coloured by chain, side view.
PDB entry 3ndb coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Structural basis of signal-sequence recognition by the signal recognition particle.
Hainzl T, Huang S, Meriläinen G, Brännström K, Sauer-Eriksson AE
Nat Struct Mol Biol 18 389-91 (2011)
PMID: 21336278

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176435 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Signal recognition particle 19 kDa protein Chain: A
Molecule details ›
Chain: A
Length: 87 amino acids
Theoretical weight: 10.38 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58440 (Residues: 1-87; Coverage: 100%)
Gene names: MJ1034, srp19
Sequence domains: SRP19 protein
Structure domains: Signal recognition particle, SRP19-like subunit
Signal recognition particle 54 kDa protein Chain: B
Molecule details ›
Chain: B
Length: 454 amino acids
Theoretical weight: 50.01 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Lactococcus lactis
UniProt:
  • Canonical: Q57565 (Residues: 3-431; Coverage: 95%)
Gene names: MJ0101, srp54
Sequence domains:
Structure domains:
SRP RNA Chain: M
Molecule details ›
Chain: M
Length: 136 nucleotides
Theoretical weight: 44.15 KDa
Sequence domains: Archaeal signal recognition particle RNA

Ligands and Environments

1 bound ligand:
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: I222
Unit cell:
a: 108.835Å b: 126.275Å c: 201.758Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.228 0.267
Expression systems:
  • Escherichia coli
  • Lactococcus lactis

Quick links

Citations

21 review citations

Signal recognition particle: an essential protein-targeting machine.
Akopian et al. (2013)
20 more

13 mentions without citation

RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
Antczak et al. (2014)
12 more