2WNU

Complex between c1q globular heads and heparan sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cutting Edge: C1Q Binds Deoxyribose and Heparan Sulfate Through Neighboring Sites of its Recognition Domain.

Garlatti, V.Chouquet, A.Lunardi, T.Vives, R.Paidassi, H.Lortat-Jacob, H.Thielens, N.M.Arlaud, G.J.Gaboriaud, C.

(2010) J.Immunol. 185: 808

  • DOI: 10.4049/jimmunol.1000184
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • C1q, the recognition subunit of the C1 complex of complement, is an archetypal pattern recognition molecule with the striking ability to sense a wide variety of targets, including a number of altered self-motifs. The recognition properties of its glo ...

    C1q, the recognition subunit of the C1 complex of complement, is an archetypal pattern recognition molecule with the striking ability to sense a wide variety of targets, including a number of altered self-motifs. The recognition properties of its globular domain were further deciphered by means of x-ray crystallography using deoxy-D-ribose and heparan sulfate as ligands. Highly specific recognition of deoxy-D-ribose, involving interactions with Arg C98, Arg C111, and Asn C113, was observed at 1.2 A resolution. Heparin-derived tetrasaccharide interacted more loosely through Lys C129, Tyr C155, and Trp C190. These data together with previous findings define a unique binding area exhibiting both polyanion and deoxy-D-ribose recognition properties, located on the inner face of C1q. DNA and heparin compete for C1q binding but are poor C1 activators compared with immune complexes. How the location of this binding area in C1q may regulate the level of C1 activation is discussed.


    Organizational Affiliation

    Laboratoire de Cristallogenese et Cristallographie des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Joseph Fourier, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C1Q SUBCOMPONENT SUBUNIT A
A, D
134Homo sapiensMutation(s): 0 
Gene Names: C1QA
Find proteins for P02745 (Homo sapiens)
Go to Gene View: C1QA
Go to UniProtKB:  P02745
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C1Q SUBCOMPONENT SUBUNIT B
B, E
136Homo sapiensMutation(s): 0 
Gene Names: C1QB
Find proteins for P02746 (Homo sapiens)
Go to Gene View: C1QB
Go to UniProtKB:  P02746
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C1Q SUBCOMPONENT SUBUNIT C
C, F
131Homo sapiensMutation(s): 0 
Gene Names: C1QC (C1QG)
Find proteins for P02747 (Homo sapiens)
Go to Gene View: C1QC
Go to UniProtKB:  P02747
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGN
Query on SGN

Download SDF File 
Download CCD File 
F
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
IDU
Query on IDU

Download SDF File 
Download CCD File 
F
2-O-sulfo-beta-L-altropyranuronic acid
C6 H10 O10 S
COJBCAMFZDFGFK-TVSWGBMESA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.090α = 92.86
b = 48.160β = 92.20
c = 87.730γ = 113.64
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance