4FQN

Crystal structure of the CCM2 C-terminal Harmonin Homology Domain (HHD)

• PDB DOI: https://doi.org/10.2210/pdb4FQN/pdb

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


• Deposited: 2012-06-25 Released: 2012-12-19 
• Deposition Author(s): Fisher, O.S., Zhang, R., Li, X., Murphy, J.W., Boggon, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Structural studies of cerebral cavernous malformations 2 (CCM2) reveal a folded helical domain at its C-terminus.

Fisher, O.S., Zhang, R., Li, X., Murphy, J.W., Demeler, B., Boggon, T.J.

(2013) FEBS Lett 587: 272-277

• PubMed: 23266514 
• DOI: https://doi.org/10.1016/j.febslet.2012.12.011
• Primary Citation of Related Structures:  
  4FQN


• PubMed Abstract: 
  

  Cerebral cavernous malformations (CCM) are neurovascular dysplasias affecting up to 0.5% of the population. Mutations in the CCM2 gene are associated with acquisition of CCM. We identify a previously uncharacterized domain at the C-terminus of CCM2 and determine its 1.9Å resolution crystal structure. Because this domain is structurally homologous to the N-terminal domain of harmonin, we name it the CCM2 harmonin-homology domain or HHD. CCM2 HHD is observed in two conformations, and we employ analytical ultracentrifugation to test its oligomerization. Additionally, CCM2 HHD contains an unusually long 13-residue 3(10) helix. This study provides the first structural characterization of CCM2.

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Organizational Affiliation: 

Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.65 kDa 
• Atom Count: 3,270 
• Modelled Residue Count: 350 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malcavernin	A, B, C, D	98	Homo sapiens	Mutation(s): 0  Gene Names: C7orf22, CCM2, PP10187
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSQ5 (Homo sapiens) Explore Q9BSQ5  Go to UniProtKB:  Q9BSQ5
PHAROS:  Q9BSQ5 GTEx:  ENSG00000136280

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.219 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/561

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.166	α = 90
b = 64.196	β = 90
c = 89.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Fisher, O.S., Zhang, R., Li, X., Murphy, J.W., Boggon, T.J.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references