3NDB

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Structural basis of signal-sequence recognition by the signal recognition particle.

Hainzl, T., Huang, S., Merilainen, G., Brannstrom, K., Sauer-Eriksson, A.E.

(2011) Nat Struct Mol Biol 18: 389-391

  • DOI: https://doi.org/10.1038/nsmb.1994
  • Primary Citation of Related Structures:  
    3NDB

  • PubMed Abstract: 

    The signal recognition particle (SRP) recognizes and binds the signal sequence of nascent proteins as they emerge from the ribosome. We present here the 3.0-Å structure of a signal sequence bound to the Methanococcus jannaschii SRP core. Structural comparison with the free SRP core shows that signal-sequence binding induces formation of the GM-linker helix and a 180° flip of the NG domain-structural changes that ensure a hierarchical succession of events during protein targeting.

    • Organizational Affiliation: 

    Department of Chemistry, Umeå University, Umeå, Sweden. tobias.hainzl@chem.umu.se


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition particle 19 kDa protein87Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ1034, srp19
UniProt
Find proteins for Q58440 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58440 
Go to UniProtKB:  Q58440
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58440
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Signal recognition 54 kDa protein454Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0101, srp54
UniProt
Find proteins for Q57565 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57565 
Go to UniProtKB:  Q57565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57565
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
SRP RNAC [auth M]136Methanocaldococcus jannaschii DSM 2661
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
D [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.835α = 90
b = 126.275β = 90
c = 201.758γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
SCALAdata scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-03-13
    Changes: Atomic model, Data collection, Derived calculations