2OVD

Crystal Structure of Human Complement Protein C8gamma with Laurate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural features of the ligand binding site on human complement protein C8gamma: A member of the lipocalin family

Chiswell, B.Lovelace, L.L.Brannen, C.Ortlund, E.A.Lebioda, L.Sodetz, J.M.

(2007) Biochim.Biophys.Acta 1774: 637-644

  • DOI: 10.1016/j.bbapap.2007.03.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human C8 is one of five components of the cytolytic membrane attack complex of complement. It contains three subunits (C8alpha, C8beta, C8gamma) arranged as a disulfide-linked C8alpha-gamma heterodimer that is noncovalently associated with C8beta. C8 ...

    Human C8 is one of five components of the cytolytic membrane attack complex of complement. It contains three subunits (C8alpha, C8beta, C8gamma) arranged as a disulfide-linked C8alpha-gamma heterodimer that is noncovalently associated with C8beta. C8gamma has the distinction of being the only lipocalin in the complement system. Lipocalins have a core beta-barrel structure forming a calyx with a binding site for a small hydrophobic ligand. A natural ligand for C8gamma has not been identified; however previous structural studies indicate C8gamma has a typical lipocalin fold that is suggestive of a ligand-binding capability. A distinctive feature of C8gamma is the division of its putative ligand binding pocket into a hydrophilic upper portion and a large hydrophobic lower cavity. Access to the latter is restricted by the close proximity of two tyrosine side chains (Y83 and Y131). In the present study, binding experiments were performed using lauric acid as a pseudoligand to investigate the potential accessibility of the lower cavity. The crystal structure of a C8gamma.laurate complex revealed that Y83 and Y131 can move to allow penetration of the hydrocarbon chain of laurate into the lower cavity. Introducing a Y83W mutation blocked access but had no effect on the ability of C8gamma to enhance C8 cytolytic activity. Together, these results indicate that the lower cavity in C8gamma could accommodate a ligand if such a ligand has a narrow hydrophobic moiety at one end. Entry of that moiety into the lower cavity would require movement of Y83 and Y131, which act as a gate at the cavity entrance.


    Organizational Affiliation

    Department of Chemistry and Biochemistry and School of Medicine, University of South Carolina, Columbia, SC 29208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement component 8, gamma polypeptide
A
182Homo sapiensMutation(s): 1 
Gene Names: C8G
Find proteins for P07360 (Homo sapiens)
Go to Gene View: C8G
Go to UniProtKB:  P07360
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAO
Query on DAO

Download SDF File 
Download CCD File 
A
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.081α = 90.00
b = 59.539β = 90.00
c = 70.836γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
SBC-Collectdata collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description