4NKN

The Crystal Structure of the N-terminal domain of COMMD9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Structural insights into the architecture and membrane interactions of the conserved COMMD proteins.

Healy, M.D., Hospenthal, M.K., Hall, R.J., Chandra, M., Chilton, M., Tillu, V., Chen, K.E., Celligoi, D.J., McDonald, F.J., Cullen, P.J., Lott, J.S., Collins, B.M., Ghai, R.

(2018) Elife 7

  • DOI: 10.7554/eLife.35898
  • Primary Citation of Related Structures:  
    4NKN, 4OE9, 6BP6

  • PubMed Abstract: 

    • The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos ...

    The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.

    Organizational Affiliation: 

    Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COMM domain-containing protein 9
A, B, C, D, E, F
A, B, C, D, E, F
121Homo sapiensMutation(s): 2 
Gene Names: COMMD9, HSPC166
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P000 (Homo sapiens)
Explore Q9P000 
Go to UniProtKB:  Q9P000
PHAROS:  Q9P000
GTEx:  ENSG00000110442 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P000
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.69α = 90
b = 79.757β = 90.61
c = 131.164γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 2.0: 2018-08-22
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary