2JG8

Crystallographic structure of human C1q globular heads complexed to phosphatidyl-serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

C1Q Binds Phosphatidylserine and Likely Acts as a Multiligand-Bridging Molecule in Apoptotic Cell Recognition.

Paidassi, H.Tacnet-Delorme, P.Garlatti, V.Darnault, C.Ghebrehiwet, B.Gaboriaud, C.Arlaud, G.J.Frachet, P.

(2008) J.Immunol. 180: 2329

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Efficient apoptotic cell clearance is critical for maintenance of tissue homeostasis, and to control the immune responses mediated by phagocytes. Little is known about the molecules that contribute "eat me" signals on the apoptotic cell surface. C1q, ...

    Efficient apoptotic cell clearance is critical for maintenance of tissue homeostasis, and to control the immune responses mediated by phagocytes. Little is known about the molecules that contribute "eat me" signals on the apoptotic cell surface. C1q, the recognition unit of the C1 complex of complement, also senses altered structures from self and is a major actor of immune tolerance. HeLa cells were rendered apoptotic by UV-B treatment and a variety of cellular and molecular approaches were used to investigate the nature of the target(s) recognized by C1q. Using surface plasmon resonance, C1q binding was shown to occur at early stages of apoptosis and to involve recognition of a cell membrane component. C1q binding and phosphatidylserine (PS) exposure, as measured by annexin V labeling, proceeded concomitantly, and annexin V inhibited C1q binding in a dose-dependent manner. As shown by cosedimentation, surface plasmon resonance, and x-ray crystallographic analyses, C1q recognized PS specifically and avidly (K(D) = 3.7-7 x 10(-8) M), through multiple interactions between its globular domain and the phosphoserine group of PS. Confocal microscopy revealed that the majority of the C1q molecules were distributed in membrane patches where they colocalized with PS. In summary, PS is one of the C1q ligands on apoptotic cells, and C1q-PS interaction takes place at early stages of apoptosis, in newly organized membrane patches. Given its versatile recognition properties, these data suggest that C1q has the unique ability to sense different markers which collectively would provide strong eat me signals, thereby allowing efficient apoptotic cell removal.


    Organizational Affiliation

    Laboratoire d'Enzymologie Mol├ęculaire, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble Cedex 1, 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
SEP
Query on SEP

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Download CCD File 
D
PHOSPHOSERINE
PHOSPHONOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SEPKd: 37 nM BINDINGMOAD
SEPKd: 500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 48.090α = 91.34
b = 48.070β = 93.34
c = 84.700γ = 113.68
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance