6RLR

Crystal structure of CD9 large extracellular loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Implications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F.

Oosterheert, W.Xenaki, K.T.Neviani, V.Pos, W.Doulkeridou, S.Manshande, J.Pearce, N.M.Kroon-Batenburg, L.M.Lutz, M.van Bergen En Henegouwen, P.M.Gros, P.

(2020) Life Sci Alliance 3

  • DOI: https://doi.org/10.26508/lsa.202000883
  • Primary Citation of Related Structures:  
    6RLR, 6Z1V, 6Z1Z, 6Z20

  • PubMed Abstract: 

    Tetraspanins are eukaryotic membrane proteins that contribute to a variety of signaling processes by organizing partner-receptor molecules in the plasma membrane. How tetraspanins bind and cluster partner receptors into tetraspanin-enriched microdomains is unknown. Here, we present crystal structures of the large extracellular loop of CD9 bound to nanobodies 4C8 and 4E8 and, the cryo-EM structure of 4C8-bound CD9 in complex with its partner EWI-F. CD9-EWI-F displays a tetrameric arrangement with two central EWI-F molecules, dimerized through their ectodomains, and two CD9 molecules, one bound to each EWI-F transmembrane helix through CD9-helices h3 and h4. In the crystal structures, nanobodies 4C8 and 4E8 bind CD9 at loops C and D, which is in agreement with the 4C8 conformation in the CD9-EWI-F complex. The complex varies from nearly twofold symmetric (with the two CD9 copies nearly anti-parallel) to ca. 50° bent arrangements. This flexible arrangement of CD9-EWI-F with potential CD9 homo-dimerization at either end provides a "concatenation model" for forming short linear or circular assemblies, which may explain the occurrence of tetraspanin-enriched microdomains.


  • Organizational Affiliation

    Department of Chemistry, Crystal and Structural Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD9 antigen
A, B, C, D
90Homo sapiensMutation(s): 0 
Gene Names: CD9MIC3TSPAN29GIG2
UniProt & NIH Common Fund Data Resources
Find proteins for P21926 (Homo sapiens)
Explore P21926 
Go to UniProtKB:  P21926
PHAROS:  P21926
GTEx:  ENSG00000010278 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21926
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.986α = 80.39
b = 39.998β = 76.29
c = 63.643γ = 68.15
Software Package:
Software NamePurpose
EVAL15data reduction
EVAL15data scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlands024.002.009

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description