3HRN | pdb_00003hrn

crystal structure of a C-terminal coiled coil domain of Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2, polycystic kidney disease 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.260 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural and molecular basis of the assembly of the TRPP2/PKD1 complex.

Yu, Y.Ulbrich, M.H.Li, M.H.Buraei, Z.Chen, X.Z.Ong, A.C.Tong, L.Isacoff, E.Y.Yang, J.

(2009) Proc Natl Acad Sci U S A 106: 11558-11563

  • DOI: https://doi.org/10.1073/pnas.0903684106
  • Primary Citation Related Structures: 
    3HRN, 3HRO

  • PubMed Abstract: 

    Mutations in PKD1 and TRPP2 account for nearly all cases of autosomal dominant polycystic kidney disease (ADPKD). These 2 proteins form a receptor/ion channel complex on the cell surface. Using a combination of biochemistry, crystallography, and a single-molecule method to determine the subunit composition of proteins in the plasma membrane of live cells, we find that this complex contains 3 TRPP2 and 1 PKD1. A newly identified coiled-coil domain in the C terminus of TRPP2 is critical for the formation of this complex. This coiled-coil domain forms a homotrimer, in both solution and crystal structure, and binds to a single coiled-coil domain in the C terminus of PKD1. Mutations that disrupt the TRPP2 coiled-coil domain trimer abolish the assembly of both the full-length TRPP2 trimer and the TRPP2/PKD1 complex and diminish the surface expression of both proteins. These results have significant implications for the assembly, regulation, and function of the TRPP2/PKD1 complex and the pathogenic mechanism of some ADPKD-producing mutations.


  • Organizational Affiliation
    • Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Macromolecule Content 

  • Total Structure Weight: 7.35 kDa 
  • Atom Count: 663 
  • Modeled Residue Count: 63 
  • Deposited Residue Count: 64 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transient receptor potential (TRP) channel subfamily P member 2 (TRPP2)64Homo sapiensMutation(s): 0 
Gene Names: PKD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13563 (Homo sapiens)
Explore Q13563 
Go to UniProtKB:  Q13563
PHAROS:  Q13563
GTEx:  ENSG00000118762 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13563
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.260 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.642α = 90
b = 43.642β = 90
c = 200.351γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description