3AJM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.bbrc.2010.07.119

  • 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 regul ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death protein 10
A, B
213Homo sapiensMutation(s): 0 
Gene Names: PDCD10 (CCM3, TFAR15)
Find proteins for Q9BUL8 (Homo sapiens)
Go to Gene View: PDCD10
Go to UniProtKB:  Q9BUL8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4IP
Query on 4IP

Download SDF File 
Download CCD File 
A
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
C6 H16 O18 P4
CIPFCGZLFXVXBG-CNWJWELYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 89.830α = 90.00
b = 89.830β = 90.00
c = 114.200γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
ADSCdata collection
SOLVEphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references