3A8N | pdb_00003a8n

Crystal structure of the Tiam1 PHCCEx domain

• PDB DOI: https://doi.org/10.2210/pdb3A8N/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-07 Released: 2009-11-24 
• Deposition Author(s): Terawaki, S., Kitano, K., Mori, T., Zhai, Y., Higuchi, Y., Itoh, N., Watanabe, T., Kaibuchi, K., Hakoshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.50 Å
• R-Value Free: 
  0.396 (Depositor), 0.400 (DCC) 
• R-Value Work: 
  0.306 (Depositor), 0.318 (DCC) 
• R-Value Observed: 
  0.306 (Depositor) 

Starting Model: experimental

Literature

The PHCCEx domain of Tiam1/2 is a novel protein- and membrane-binding module

Terawaki, S., Kitano, K., Mori, T., Zhai, Y., Higuchi, Y., Itoh, N., Watanabe, T., Kaibuchi, K., Hakoshima, T.

(2010) EMBO J 29: 236-250

• PubMed: 19893486 
• DOI: https://doi.org/10.1038/emboj.2009.323
• Primary Citation Related Structures: 
  3A8N, 3A8P, 3A8Q


• PubMed Abstract: 
  

  Tiam1 and Tiam2 (Tiam1/2) are guanine nucleotide-exchange factors that possess the PH-CC-Ex (pleckstrin homology, coiled coil and extra) region that mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. Crystal structures of the PH-CC-Ex regions revealed a single globular domain, PHCCEx domain, comprising a conventional PH subdomain associated with an antiparallel coiled coil of CC subdomain and a novel three-helical globular Ex subdomain. The PH subdomain resembles the beta-spectrin PH domain, suggesting non-canonical phosphatidylinositol binding. Mutational and binding studies indicated that CC and Ex subdomains form a positively charged surface for protein binding. We identified two unique acidic sequence motifs in Tiam1/2-interacting proteins for binding to PHCCEx domain, Motif-I in CD44 and ephrinB's and the NMDA receptor, and Motif-II in Par3 and JIP2. Our results suggest the molecular basis by which the Tiam1/2 PHCCEx domain facilitates dual binding to membranes and signalling proteins.

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Organizational Affiliation: 
• Structural Biology Laboratory, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.62 kDa 
• Atom Count: 1,142 
• Modeled Residue Count: 230 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-lymphoma invasion and metastasis-inducing protein 1	A	279	Mus musculus	Mutation(s): 0  Gene Names: Tiam1, Tiam-1
UniProt & NIH Common Fund Data Resources
Find proteins for Q60610 (Mus musculus) Explore Q60610  Go to UniProtKB:  Q60610
IMPC:  MGI:103306

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.50 Å
• R-Value Free:  0.396 (Depositor), 0.400 (DCC) 
• R-Value Work:  0.306 (Depositor), 0.318 (DCC) 
• R-Value Observed: 0.306 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.47	α = 90
b = 113.47	β = 90
c = 113.837	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Terawaki, S., Kitano, K., Mori, T., Zhai, Y., Higuchi, Y., Itoh, N., Watanabe, T., Kaibuchi, K., Hakoshima, T.

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description