3NDB | pdb_00003ndb

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

• PDB DOI: https://doi.org/10.2210/pdb3NDB/pdb
• NAKB: 3NDB

• Classification: SIGNALING PROTEIN/RNA
• Organism(s): Methanocaldococcus jannaschii, Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli, Lactococcus lactis
• Mutation(s): No 


• Deposited: 2010-06-07 Released: 2011-02-23 
• Deposition Author(s): Hainzl, T., Huang, S., Sauer-Eriksson, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.267 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

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

• PubMed: 21336278 
• DOI: https://doi.org/10.1038/nsmb.1994
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Umeå University, Umeå, Sweden. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.63 kDa 
• Atom Count: 6,926 
• Modeled Residue Count: 643 
• Deposited Residue Count: 677 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle 19 kDa protein	A	87	Methanocaldococcus jannaschii	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition 54 kDa protein	B	454	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: MJ0101, srp54 EC: 3.6.5.4
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 ID: 3
Molecule	Chains	Length	Organism	Image
SRP RNA	C [auth M]	136	Methanocaldococcus jannaschii DSM 2661

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	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 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.835	α = 90
b = 126.275	β = 90
c = 201.758	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Hainzl, T., Huang, S., Sauer-Eriksson, E.

Revision History  

• 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