3TVD | pdb_00003tvd

Crystal Structure of Mouse RhoA-GTP complex

• PDB DOI: https://doi.org/10.2210/pdb3TVD/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-20 Released: 2012-10-10 
• Deposition Author(s): Swaminathan, K., Pal, K., Jobichen, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.282 (Depositor) 
• R-Value Work: 
  0.223 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of mouse RhoA:GTPgammaS complex in a centered lattice.

Jobichen, C., Pal, K., Swaminathan, K.

(2012) J Struct Funct Genomics 13: 241-245

• PubMed: 23001747 
• DOI: https://doi.org/10.1007/s10969-012-9143-5
• Primary Citation Related Structures: 
  3TVD


• PubMed Abstract: 
  

  RhoA, a member of the Rho sub-family of small GTPases, plays a significant signaling role in cell morphogenesis, migration, neuronal development, cell division and adhesion. So far, 4 structures of RhoA:GDP/GTP analogs and 14 structures of RhoA in complex with other proteins have been reported. All RhoA:GDP/GTP analog complexes have been crystallized in primitive lattices and RhoA is monomeric. This is the first time a RhoA:GTP analog complex has been crystallized as a dimer in a centered lattice. The present structure reveals structural differences in the switch-I (residues 28-42) and switch-II (residues 61-66) regions, which play important roles in interactions with downstream targets to transduce signals, when compared to the previously reported structures.

---

Organizational Affiliation: 
• Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.75 kDa 
• Atom Count: 2,940 
• Modeled Residue Count: 360 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	A, B	193	Rattus norvegicus	Mutation(s): 0  Gene Names: Arha, Arha2, Rhoa EC: 3.6.5.2
UniProt
Find proteins for P61589 (Rattus norvegicus) Explore P61589  Go to UniProtKB:  P61589

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSP	C [auth A], E [auth B]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.282 (Depositor) 
• R-Value Work:  0.223 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.813	α = 90
b = 122.652	β = 90
c = 91.276	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Swaminathan, K., Pal, K., Jobichen, C.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description