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PDBsum entry 1ok2

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protein ligands Protein-protein interface(s) links
Regulator of complement pathway PDB id
1ok2
Jmol PyMol
Contents
Protein chain
254 a.a. *
Ligands
ACT ×4
SO4 ×2
GOL ×9
Waters ×275
* Residue conservation analysis
PDB id:
1ok2
Name: Regulator of complement pathway
Title: Decay accelerating factor (cd55): the structure of an intact human complement regulator.
Structure: Complement decay-accelerating factor. Chain: a, b. Fragment: four extracellular scr domains residues 35-285. Synonym: cd55, cr, daf. Engineered: yes. Other_details: modelled glycerols, acetates and sulphates from crystallisation buffer
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: human sequence expressed in e.Coli.
Biol. unit: Dimer (from PDB file)
Resolution:
2.5Å     R-factor:   0.229     R-free:   0.274
Authors: P.Lukacik,P.Roversi,J.White,D.Esser,G.P.Smith,J.Billington, P.A.Williams,P.M.Rudd,M.R.Wormald,M.D.M.Crispin, C.M.Radcliffe,R.A.Dwek,D.J.Evans,B.P.Morgan,R.A.G.Smith, S.M.Lea
Key ref:
P.Lukacik et al. (2004). Complement regulation at the molecular level: the structure of decay-accelerating factor. Proc Natl Acad Sci U S A, 101, 1279-1284. PubMed id: 14734808 DOI: 10.1073/pnas.0307200101
Date:
16-Jul-03     Release date:   07-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08174  (DAF_HUMAN) -  Complement decay-accelerating factor
Seq:
Struc:
381 a.a.
254 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1073/pnas.0307200101 Proc Natl Acad Sci U S A 101:1279-1284 (2004)
PubMed id: 14734808  
 
 
Complement regulation at the molecular level: the structure of decay-accelerating factor.
P.Lukacik, P.Roversi, J.White, D.Esser, G.P.Smith, J.Billington, P.A.Williams, P.M.Rudd, M.R.Wormald, D.J.Harvey, M.D.Crispin, C.M.Radcliffe, R.A.Dwek, D.J.Evans, B.P.Morgan, R.A.Smith, S.M.Lea.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structure of CD55. (a) Structure of the four SCR domains (views at 0° and 90°). The molecule shown is molecule A from crystal form A (see Table 2). The structure is colored from blue at the N terminus to red at the C terminus. All figures were drawn with AESOP (M. E. M. Noble, unpublished program). (b) Comparison between eight copies of CD55[1234] from three different crystal forms. The molecules are overlaid with carbons from SCR domain 3 (residues 126-185) so that the lack of variation in the SCR 2/3 domain interface may be appreciated, and the molecules are colored so that the two copies from crystal forms A and B are red and green, respectively, and the four copies from crystal form C are blue. (c) Full model for CD55 in the cell membrane. This model combines the atomic coordinates for the SCR domains with models for the N- and O-linked sugars and the GPI anchor, built as described in the text. The molecule is embedded in a lipid monolayer to allow the extension of the stalk that supports the SCR domains above the membrane to be visualized.
Figure 3.
Fig. 3. Model of the complex between CD55 and the von Willebrand factor type A domain (vWF-A) of factor B. b and d show two views of the complex between CD55 and the vWF-A domain of factor B generated as described in the text. CD55 is oriented as in Fig. 1a Left. b shows a surface representation, and d shows a secondary structure trace for both molecules, which are colored as follows: CD55, the hydrophobic potential was calculated by using the program GRID and mapped onto the surface in AESOP (43) colored from green (most favorable for hydrophobic probe interaction) via yellow to white; and vWF-A of factor B, residues implicated in CD55 binding are colored red, and those implicated in C3b binding are colored orange; positions where mutation has no effect on CD55 sensitivity are colored blue. a and c show each molecule rotated 90° away from the view shown in b to allow inspection of the surfaces buried in the interface. CD55 is shown in the same view as in that of Fig. 1a Right.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21175663 N.M.Burton, and G.Daniels (2011).
Structural modelling of red cell surface proteins.
  Vox Sang, 100, 129-139.  
20806220 T.A.Jowitt, A.D.Murdoch, C.Baldock, R.Berry, J.M.Day, and T.E.Hardingham (2010).
Order within disorder: aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered.
  Proteins, 78, 3317-3327.  
19640995 A.K.Singh, V.N.Yadav, K.Pyaram, J.Mullick, and A.Sahu (2009).
Mapping of functional domains in herpesvirus saimiri complement control protein homolog: complement control protein domain 2 is the smallest structural unit displaying cofactor and decay-accelerating activities.
  J Virol, 83, 10299-10304.  
19503104 J.Wu, Y.Q.Wu, D.Ricklin, B.J.Janssen, J.D.Lambris, and P.Gros (2009).
Structure of complement fragment C3b-factor H and implications for host protection by complement regulators.
  Nat Immunol, 10, 728-733.
PDB code: 2wii
19258706 P.Karnchanaphanurach, R.Mirchev, I.Ghiran, J.M.Asara, B.Papahadjopoulos-Sternberg, A.Nicholson-Weller, and D.E.Golan (2009).
C3b deposition on human erythrocytes induces the formation of a membrane skeleton-linked protein complex.
  J Clin Invest, 119, 788-801.  
18559962 H.Ashida, R.Maki, H.Ozawa, Y.Tani, M.Kiyohara, M.Fujita, A.Imamura, H.Ishida, M.Kiso, and K.Yamamoto (2008).
Characterization of two different endo-alpha-N-acetylgalactosaminidases from probiotic and pathogenic enterobacteria, Bifidobacterium longum and Clostridium perfringens.
  Glycobiology, 18, 727-734.  
18252712 H.G.Hocking, A.P.Herbert, D.Kavanagh, D.C.Soares, V.P.Ferreira, M.K.Pangburn, D.Uhrín, and P.N.Barlow (2008).
Structure of the N-terminal region of complement factor H and conformational implications of disease-linked sequence variations.
  J Biol Chem, 283, 9475-9487.
PDB codes: 2rlp 2rlq
18197169 J.D.Lambris, D.Ricklin, and B.V.Geisbrecht (2008).
Complement evasion by human pathogens.
  Nat Rev Microbiol, 6, 132-142.  
17804498 S.Hafenstein, V.D.Bowman, P.R.Chipman, C.M.Bator Kelly, F.Lin, M.E.Medof, and M.G.Rossmann (2007).
Interaction of decay-accelerating factor with coxsackievirus B3.
  J Virol, 81, 12927-12935.
PDB codes: 2qzd 2qzf 2qzh
16784816 J.H.Mikesch, H.Buerger, R.Simon, and B.Brandt (2006).
Decay-accelerating factor (CD55): a versatile acting molecule in human malignancies.
  Biochim Biophys Acta, 1766, 42-52.  
16473914 L.Zhang, and D.Morikis (2006).
Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics.
  Biophys J, 90, 3106-3119.  
15831825 A.L.Servin (2005).
Pathogenesis of Afa/Dr diffusely adhering Escherichia coli.
  Clin Microbiol Rev, 18, 264-292.  
15958123 H.J.Willison (2005).
The immunobiology of Guillain-Barré syndromes.
  J Peripher Nerv Syst, 10, 94.  
15572774 E.Blanc, P.Roversi, C.Vonrhein, C.Flensburg, S.M.Lea, and G.Bricogne (2004).
Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.
  Acta Crystallogr D Biol Crystallogr, 60, 2210-2221.  
15507647 E.S.Johansson, L.Xing, R.H.Cheng, and D.R.Shafren (2004).
Enhanced cellular receptor usage by a bioselected variant of coxsackievirus a21.
  J Virol, 78, 12603-12612.  
15322283 J.White, P.Lukacik, D.Esser, M.Steward, N.Giddings, J.R.Bright, S.J.Fritchley, B.P.Morgan, S.M.Lea, G.P.Smith, and R.A.Smith (2004).
Biological activity, membrane-targeting modification, and crystallization of soluble human decay accelerating factor expressed in E. coli.
  Protein Sci, 13, 2406-2415.  
15103144 R.J.Abbott, V.Knott, P.Roversi, S.Neudeck, P.Lukacik, P.A.Handford, and S.M.Lea (2004).
Crystallization and preliminary X-ray diffraction analysis of three EGF domains of EMR2, a 7TM immune-system molecule.
  Acta Crystallogr D Biol Crystallogr, 60, 936-938.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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