2WNV

Complex between C1q globular heads and deoxyribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C1Q SUBCOMPONENT SUBUNIT AA, D134Homo sapiensMutation(s): 0 
Gene Names: C1QA
Find proteins for P02745 (Homo sapiens)
Explore P02745 
Go to UniProtKB:  P02745
NIH Common Fund Data Resources
PHAROS  P02745
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C1Q SUBCOMPONENT SUBUNIT BB, E136Homo sapiensMutation(s): 0 
Gene Names: C1QB
Find proteins for P02746 (Homo sapiens)
Explore P02746 
Go to UniProtKB:  P02746
NIH Common Fund Data Resources
PHAROS  P02746
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C1Q SUBCOMPONENT SUBUNIT CC, F131Homo sapiensMutation(s): 0 
Gene Names: C1QCC1QG
Find proteins for P02747 (Homo sapiens)
Explore P02747 
Go to UniProtKB:  P02747
NIH Common Fund Data Resources
PHAROS  P02747
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
2DR
Query on 2DR

Download CCD File 
C
2-deoxy-beta-D-erythro-pentofuranose
C5 H10 O4
PDWIQYODPROSQH-VPENINKCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.35α = 92.39
b = 48.33β = 92.6
c = 88.06γ = 113.57
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary