1H04 | pdb_00001h04

Human CD55 domains 3 & 4

• PDB DOI: https://doi.org/10.2210/pdb1H04/pdb

• Classification: IMMUNE SYSTEM PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2002-06-11 Released: 2003-03-20 
• Deposition Author(s): Williams, P., Chaudhry, Y., Goodfellow, I., Billington, J., Spiller, B., Evans, D.J., Lea, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.259 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Mapping Cd55 Function. The Structure of Two Pathogen-Binding Domains at 1.7 A

Williams, P., Chaudhry, Y., Goodfellow, I., Billington, J., Powell, R., Spiller, O., Evans, D.J., Lea, S.M.

(2003) J Biological Chem 278: 10691

• PubMed: 12499389 
• DOI: https://doi.org/10.1074/jbc.M212561200
• Primary Citation Related Structures: 
  1H03, 1H04, 1H2P, 1H2Q, 1UOT


• PubMed Abstract: 
  

  Decay-accelerating factor (CD55), a regulator of the alternative and classical pathways of complement activation, is expressed on all serum-exposed cells. It is used by pathogens, including many enteroviruses and uropathogenic Escherichia coli, as a receptor prior to infection. We describe the x-ray structure of a pathogen-binding fragment of human CD55 at 1.7 A resolution containing two of the three domains required for regulation of human complement. We have used mutagenesis to map biological functions onto the molecule; decay-accelerating activity maps to a single face of the molecule, whereas bacterial and viral pathogens recognize a variety of different sites on CD55.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 13.37 kDa 
• Atom Count: 1,063 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COMPLEMENT DECAY-ACCELERATING FACTOR	A [auth P]	125	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P08174 (Homo sapiens) Explore P08174  Go to UniProtKB:  P08174
PHAROS:  P08174 GTEx:  ENSG00000196352

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	B [auth P]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.259 (Depositor) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.7	α = 90
b = 20.4	β = 111.5
c = 52.7	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-20 
Deposition Author(s): Williams, P., Chaudhry, Y., Goodfellow, I., Billington, J., Spiller, B., Evans, D.J., Lea, S.M.

Revision History  

• Version 1.0: 2003-03-20
  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: 2023-12-13
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary