5TCX

Crystal structure of human tetraspanin CD81


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.955 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket.

Zimmerman, B.Kelly, B.McMillan, B.J.Seegar, T.C.Dror, R.O.Kruse, A.C.Blacklow, S.C.

(2016) Cell 167: 1041-1051.e11

  • DOI: 10.1016/j.cell.2016.09.056

  • PubMed Abstract: 
  • Tetraspanins comprise a diverse family of four-pass transmembrane proteins that play critical roles in the immune, reproductive, genitourinary, and auditory systems. Despite their pervasive roles in human physiology, little is known about the structu ...

    Tetraspanins comprise a diverse family of four-pass transmembrane proteins that play critical roles in the immune, reproductive, genitourinary, and auditory systems. Despite their pervasive roles in human physiology, little is known about the structure of tetraspanins or the molecular mechanisms underlying their various functions. Here, we report the crystal structure of human CD81, a full-length tetraspanin. The transmembrane segments of CD81 pack as two largely separated pairs of helices, capped by the large extracellular loop (EC2) at the outer membrane leaflet. The two pairs of helices converge at the inner leaflet to create an intramembrane pocket with additional electron density corresponding to a bound cholesterol molecule within the cavity. Molecular dynamics simulations identify an additional conformation in which EC2 separates substantially from the transmembrane domain. Cholesterol binding appears to modulate CD81 activity in cells, suggesting a potential mechanism for regulation of tetraspanin function.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD81 antigen
A
246Homo sapiensMutation(s): 4 
Gene Names: CD81 (TAPA1, TSPAN28)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Tetraspanins
Protein: 
CD81 full-length tetraspanin
Find proteins for P60033 (Homo sapiens)
Go to Gene View: CD81
Go to UniProtKB:  P60033
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.955 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.430α = 90.00
b = 73.510β = 125.11
c = 70.350γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited States5RO1 CA092433
National Institutes of Health/Office of the DirectorUnited States1DP5 OD021345

Revision History 

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence