2V8E

Crystal structure of Human Complement Factor H, SCR domains 6-8 (H402 risk variant), in complex with ligand.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for Complement Factor H Linked Age-Related Macular Degeneration.

Prosser, B.E.Johnson, S.Roversi, P.Herbert, A.P.Blaum, B.S.Tyrrell, J.Jowitt, T.A.Clark, S.J.Tarelli, E.Uhrin, D.Barlow, P.N.Sim, R.B.Day, A.J.Lea, S.M.

(2007) J.Exp.Med. 204: 2277

  • DOI: 10.1084/jem.20071069
  • Primary Citation of Related Structures:  2UWN

  • PubMed Abstract: 
  • Nearly 50 million people worldwide suffer from age-related macular degeneration (AMD), which causes severe loss of central vision. A single-nucleotide polymorphism in the gene for the complement regulator factor H (FH), which causes a Tyr-to-His subs ...

    Nearly 50 million people worldwide suffer from age-related macular degeneration (AMD), which causes severe loss of central vision. A single-nucleotide polymorphism in the gene for the complement regulator factor H (FH), which causes a Tyr-to-His substitution at position 402, is linked to approximately 50% of attributable risks for AMD. We present the crystal structure of the region of FH containing the polymorphic amino acid His402 in complex with an analogue of the glycosaminoglycans (GAGs) that localize the complement regulator on the cell surface. The structure demonstrates direct coordination of ligand by the disease-associated polymorphic residue, providing a molecular explanation of the genetic observation. This glycan-binding site occupies the center of an extended interaction groove on the regulator's surface, implying multivalent binding of sulfated GAGs. This finding is confirmed by structure-based site-directed mutagenesis, nuclear magnetic resonance-monitored binding experiments performed for both H402 and Y402 variants with this and another model GAG, and analysis of an extended GAG-FH complex.


    Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, England, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT FACTOR H
A
187Homo sapiensGene Names: CFH (HF, HF1, HF2)
Find proteins for P08603 (Homo sapiens)
Go to Gene View: CFH
Go to UniProtKB:  P08603
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SCR
Query on SCR

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Download CCD File 
A
SUCROSE OCTASULFATE
C12 H22 O35 S8
WEPNHBQBLCNOBB-UGDNZRGBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.000α = 90.00
b = 92.500β = 90.00
c = 57.100γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
DMmodel building
PIRATEphasing
MOLREPphasing
BUSTER-TNTphasing
MOSFLMdata reduction
DMphasing
SHARP-SOLOMONphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance