1OK1 | pdb_00001ok1

Decay accelerating factor (cd55) : the structure of an intact human complement regulator.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.260 (DCC) 
  • R-Value Work: 
    0.203 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1OK1

This is version 1.4 of the entry. See complete history

Literature

Complement Regulation at the Molecular Level: The Structure of Decay-Accelerating Factor

Lukacik, P.Roversi, P.White, J.Esser, D.Smith, G.P.Billington, J.Williams, P.A.Rudd, P.M.Wormald, M.R.Harvey, D.J.Crispin, M.D.M.Radcliffe, C.M.Dwek, R.A.Evans, D.J.Morgan, B.P.Smith, R.A.G.Lea, S.M.

(2004) Proc Natl Acad Sci U S A 101: 1279

  • DOI: https://doi.org/10.1073/pnas.0307200101
  • Primary Citation Related Structures: 
    1OJV, 1OJW, 1OJY, 1OK1, 1OK2, 1OK3, 1OK9

  • PubMed Abstract: 

    The human complement regulator CD55 is a key molecule protecting self-cells from complement-mediated lysis. X-ray diffraction and analytical ultracentrifugation data reveal a rod-like arrangement of four short consensus repeat (SCR) domains in both the crystal and solution. The stalk linking the four SCR domains to the glycosylphosphatidylinositol anchor is extended by the addition of 11 highly charged O-glycans and positions the domains an estimated 177 A above the membrane. Mutation mapping and hydrophobic potential analysis suggest that the interaction with the convertase, and thus complement regulation, depends on the burial of a hydrophobic patch centered on the linker between SCR domains 2 and 3.


  • Organizational Affiliation
    • Laboratory of Molecular Biophysics and Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England.

Macromolecule Content 

  • Total Structure Weight: 57.61 kDa 
  • Atom Count: 4,277 
  • Modeled Residue Count: 507 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COMPLEMENT DECAY-ACCELERATING FACTOR
A, B
254Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08174 (Homo sapiens)
Explore P08174 
Go to UniProtKB:  P08174
PHAROS:  P08174
GTEx:  ENSG00000196352 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08174
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
J [auth B],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.260 (DCC) 
  • R-Value Work:  0.203 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.034α = 86.85
b = 55.133β = 84.92
c = 62.001γ = 65.03
Software Package:
Software NamePurpose
SHARPmodel building
TNTrefinement
SCALAdata scaling
MOLREPphasing
BUSTERphasing
TNTphasing
SHARPphasing
DMphasing
SOLOMONphasing
SIGMAAphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-07
    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, Other, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary