Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20637.39 
• Atom Count: 1427 
• Residue Count: 180 
• Unique protein chains: 1

1DPF

CRYSTAL STRUCTURE OF A MG-FREE FORM OF RHOA COMPLEXED WITH GDP

• DOI: 10.2210/pdb1DPF/pdb

• Classification: GENE REGULATION/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 1999-12-27 Released: 2000-06-21 
• Deposition Author(s): Shimizu, T., Ihara, K., Maesaki, R., Kuroda, S., Kaibuchi, K., Hakoshima, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.252 
• R-Value Work: 0.201 

Literature

An open conformation of switch I revealed by the crystal structure of a Mg2+-free form of RHOA complexed with GDP. Implications for the GDP/GTP exchange mechanism.

Shimizu, T., Ihara, K., Maesaki, R., Kuroda, S., Kaibuchi, K., Hakoshima, T.

(2000) J.Biol.Chem. 275: 18311-18317

• PubMed: 10748207 
• DOI: 10.1074/jbc.M910274199


• PubMed Abstract: 
  

Mg(2+) ions are essential for guanosine triphosphatase (GTPase) activity and play key roles in guanine nucleotide binding and preserving the structural integrity of GTP-binding proteins. We determined the crystal structure of a small GTPase RHOA complexed with GDP in the absence of Mg(2+) at 2.0-A resolution. Elimination of a Mg(2+) ion induces significant conformational changes in the switch I region that opens up the nucleotide-binding site. Similar structural changes have been observed in the switch regions of Ha-Ras bound to its guanine nucleotide exchange factor, Sos. This RHOA-GDP structure reveals an important regulatory role for Mg(2+) and suggests that guanine nucleotide exchange factor may utilize this feature of switch I to produce an open conformation in GDP/GTP exchange.

---

Organizational Affiliation: 

Division of Strucural Biology and Signal Transduction, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RHOA	A	180	Homo sapiens	Mutations: V14G Gene Names: RHOA (ARH12, ARHA, RHO12)
Find proteins for P61586 (Homo sapiens) Go to Gene View: RHOA Go to UniProtKB:  P61586

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	A	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.252 
• R-Value Work: 0.201 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 91.200	α = 90.00
b = 91.200	β = 90.00
c = 56.500	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-27 
• Released Date: 2000-06-21 
• Deposition Author(s): Shimizu, T., Ihara, K., Maesaki, R., Kuroda, S., Kaibuchi, K., Hakoshima, T.

Revision History 

• Version 1.0: 2000-06-21
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-03-14
  Type: Database references