8S1N | pdb_00008s1n

Crystal structure of human Rac1-GDP

• PDB DOI: https://doi.org/10.2210/pdb8S1N/pdb

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


• Deposited: 2024-02-15 Released: 2025-09-03 
• Deposition Author(s): Ferrandez, Y., Nawrotek, A., Cherfils, J.
• Funding Organization(s): Centre National de la Recherche Scientifique (CNRS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of GDP form of Rac1

Ferrandez, Y., Nawrotek, A., Cherfils, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.18 kDa 
• Atom Count: 1,467 
• Modeled Residue Count: 172 
• Deposited Residue Count: 177 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A	177	Homo sapiens	Mutation(s): 0  Gene Names: RAC1, TC25, MIG5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000 GTEx:  ENSG00000136238

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.258 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.489	α = 90
b = 90.34	β = 90
c = 107.405	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
MxCuBE	data collection
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Ferrandez, Y., Nawrotek, A., Cherfils, J.

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Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release