1JPJ

GMPPNP Complex of SRP GTPase NG Domain

• PDB DOI: https://doi.org/10.2210/pdb1JPJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-08-02 Released: 2002-02-02 
• Deposition Author(s): Padmanabhan, S., Freymann, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.306 
• R-Value Work: 0.201 

Literature

The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.

Padmanabhan, S., Freymann, D.M.

(2001) Structure 9: 859-867

• PubMed: 11566135 
• DOI: https://doi.org/10.1016/s0969-2126(01)00641-4
• Primary Citation of Related Structures:  
  1JPJ, 1JPN


• PubMed Abstract: 
  

  The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein that mediates cotranslational targeting of secreted and membrane proteins to the membrane. Targeting is regulated by GTP binding and hydrolysis events that require direct interaction between structurally homologous "NG" GTPase domains of the SRP signal recognition subunit and its membrane-associated receptor, SR alpha. Structures of both the apo and GDP bound NG domains of the prokaryotic SRP54 homolog, Ffh, and the prokaryotic receptor homolog, FtsY, have been determined. The structural basis for the GTP-dependent interaction between the two proteins, however, remains unknown.

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Organizational Affiliation: 

Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Medical School, Chicago, IL 60611, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.99 kDa 
• Atom Count: 2,357 
• Modelled Residue Count: 294 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL RECOGNITION PARTICLE PROTEIN	A	296	Thermus aquaticus	Mutation(s): 0
UniProt
Find proteins for O07347 (Thermus aquaticus) Explore O07347  Go to UniProtKB:  O07347

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.306 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.69	α = 90
b = 60.41	β = 90
c = 86.06	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-02 
Deposition Author(s): Padmanabhan, S., Freymann, D.M.

Revision History  

• Version 1.0: 2002-02-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description