1XM9

Structure of the armadillo repeat domain of plakophilin 1

• PDB DOI: https://doi.org/10.2210/pdb1XM9/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-10-01 Released: 2005-03-22 
• Deposition Author(s): Choi, H.J., Weis, W.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.324 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Literature

Structure of the armadillo repeat domain of plakophilin 1.

Choi, H.J., Weis, W.I.

(2005) J Mol Biol 346: 367-376

• PubMed: 15663951 
• DOI: https://doi.org/10.1016/j.jmb.2004.11.048
• Primary Citation of Related Structures:  
  1XM9


• PubMed Abstract: 
  

  The p120ctn subfamily of armadillo domain proteins has roles in modulating intercellular adhesion by cadherin-containing junctions. We have determined the crystal structure of the arm repeat domain from plakophilin-1 (PKP1), a member of the p120ctn subfamily that is found in desmosomes. The structure reveals that the domain has nine instead of the expected ten arm repeats. A sequence predicted to be an arm repeat is instead a large insert which serves as a wedge that produces a significant bend in the overall domain structure. Structure-based sequence alignments indicate that the nine repeats and large insert are common to this subfamily of armadillo proteins. A prominent basic patch on the surface of the protein may serve as a binding site for partners of these proteins.

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Organizational Affiliation: 

Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive West, Stanford, CA 94305-5126, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.49 kDa 
• Atom Count: 3,237 
• Modelled Residue Count: 420 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
plakophilin 1	A	457	Homo sapiens	Mutation(s): 0  Gene Names: PKP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13835 (Homo sapiens) Explore Q13835  Go to UniProtKB:  Q13835
PHAROS:  Q13835 GTEx:  ENSG00000081277

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.324 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.355	α = 90
b = 131.977	β = 90
c = 142.044	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-22 
Deposition Author(s): Choi, H.J., Weis, W.I.

Revision History  

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references