6TM1 | pdb_00006tm1

Crystal structure of the DHR2 domain of DOCK10 in complex with RAC3

• PDB DOI: https://doi.org/10.2210/pdb6TM1/pdb

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


• Deposited: 2019-12-03 Released: 2020-01-22 
• Deposition Author(s): Barford, D., Fan, D., Cronin, N., Yang, J.
• Funding Organization(s): Cancer Research UK

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.71 Å
• R-Value Free: 
  0.321 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Models: experimental

Literature

Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10

Fan, D., Yang, J., Cronin, N., Barford, D.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.06.15.496229

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 127.52 kDa 
• Atom Count: 6,775 
• Modelled Residue Count: 977 
• Deposited Residue Count: 1,107 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 10	A [auth B]	457	Homo sapiens	Mutation(s): 0  Gene Names: DOCK10, KIAA0694, ZIZ3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BY6 (Homo sapiens) Explore Q96BY6  Go to UniProtKB:  Q96BY6
PHAROS:  Q96BY6 GTEx:  ENSG00000135905

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 3	B [auth A]	192	Homo sapiens	Mutation(s): 0  Gene Names: RAC3 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60763 (Homo sapiens) Explore P60763  Go to UniProtKB:  P60763
PHAROS:  P60763 GTEx:  ENSG00000169750

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 10	C	458	Homo sapiens	Mutation(s): 0  Gene Names: DOCK10, KIAA0694, ZIZ3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BY6 (Homo sapiens) Explore Q96BY6  Go to UniProtKB:  Q96BY6
PHAROS:  Q96BY6 GTEx:  ENSG00000135905

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.71 Å
• R-Value Free:  0.321 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.079	α = 90
b = 128.455	β = 90
c = 215.102	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Barford, D., Fan, D., Cronin, N., Yang, J.

---

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C576/A14109

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description