Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 50.29 kDa 
• Atom Count: 3318 
• Residue Count: 391 
• Unique protein chains: 1

3AJM

Crystal structure of programmed cell death 10 in complex with inositol 1,3,4,5-tetrakisphosphate

• DOI: 10.2210/pdb3AJM/pdb

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


• Deposited: 2010-06-09 Released: 2010-06-30 
• Deposition Author(s): Ding, J., Wang, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.264 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Crystal structure of human programmed cell death 10 complexed with inositol-(1,3,4,5)-tetrakisphosphate: a novel adaptor protein involved in human cerebral cavernous malformation.

Ding, J., Wang, X., Li, D.F., Hu, Y., Zhang, Y., Wang, D.C.

(2010) Biochem Biophys Res Commun 399: 587-592

• PubMed: 20682288 
• DOI: 10.1016/j.bbrc.2010.07.119
• Primary Citation of Related Structures:  
  3AJM


• PubMed Abstract: 
  

Programmed cell death 10 (PDCD10) is a novel adaptor protein involved in human cerebral cavernous malformation, a common vascular lesion mostly occurring in the central nervous system. By interacting with different signal proteins, PDCD10 could regulate various physiological processes in the cell. The crystal structure of human PDCD10 complexed with inositol-(1,3,4,5)-tetrakisphosphate has been determined at 2.3A resolution. The structure reveals an integrated dimer via a unique assembly that has never been observed before. Each PDCD10 monomer contains two independent domains: an N-terminal domain with a new fold involved in the tight dimer assembly and a C-terminal four-helix bundle domain that closely resembles the focal adhesion targeting domain of focal adhesion kinase. An eight-residue flexible linker connects the two domains, potentially conferring mobility onto the C-terminal domain, resulting in the conformational variability of PDCD10. A variable basic cleft on the top of the dimer interface binds to phosphatidylinositide and regulates the intracellular localization of PDCD10. Two potential sites, respectively located on the two domains, are critical for recruiting different binding partners, such as germinal center kinase III proteins and the focal adhesion protein paxillin.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 10	A, B	213	Homo sapiens	Mutation(s): 0  Gene Names: PDCD10, CCM3, TFAR15
Find proteins for Q9BUL8 (Homo sapiens) Explore Q9BUL8  Go to UniProtKB:  Q9BUL8
NIH Common Fund Data Resources
PHAROS:  Q9BUL8 GTEx:  ENSG00000114209

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4IP	A	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C6 H16 O18 P4 CIPFCGZLFXVXBG-CNWJWELYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.264 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.83	α = 90
b = 89.83	β = 90
c = 114.2	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-09 
• Released Date: 2010-06-30 
Deposition Author(s): Ding, J., Wang, D.C.

Revision History 

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references