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PDBsum entry 1ghq
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protein ligands metals Protein-protein interface(s) links
Immune system/viral protein receptor PDB id
1ghq

 

 

 

 

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Contents
Protein chains
307 a.a. *
129 a.a. *
Ligands
NDG ×2
Metals
_ZN ×2
Waters ×666
* Residue conservation analysis
PDB id:
1ghq
Name: Immune system/viral protein receptor
Title: Cr2-c3d complex structure
Structure: Complement c3. Chain: a. Fragment: fragment of alpha chain. Mutation: yes. Cr2/cd121/c3d/epstein-barr virus receptor. Chain: b, c. Fragment: sequence database residues 21-153
Source: Homo sapiens. Human. Organism_taxid: 9606. Organism_taxid: 9606
Biol. unit: Hexamer (from PQS)
Resolution:
2.04Å     R-factor:   0.195     R-free:   0.239
Authors: G.Szakonyi,J.M.Guthridge,D.Li,V.M.Holers,X.S.Chen
Key ref:
G.Szakonyi et al. (2001). Structure of complement receptor 2 in complex with its C3d ligand. Science, 292, 1725-1728. PubMed id: 11387479 DOI: 10.1126/science.1059118
Date:
11-Jan-01     Release date:   13-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01024  (CO3_HUMAN) -  Complement C3 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1663 a.a.
307 a.a.*
Protein chains
Pfam   ArchSchema ?
P20023  (CR2_HUMAN) -  Complement receptor type 2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1033 a.a.
129 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 

 
DOI no: 10.1126/science.1059118 Science 292:1725-1728 (2001)
PubMed id: 11387479  
 
 
Structure of complement receptor 2 in complex with its C3d ligand.
G.Szakonyi, J.M.Guthridge, D.Li, K.Young, V.M.Holers, X.S.Chen.
 
  ABSTRACT  
 
Complement receptor 2 (CR2/CD21) is an important receptor that amplifies B lymphocyte activation by bridging the innate and adaptive immune systems. CR2 ligands include complement C3d and Epstein-Barr virus glycoprotein 350/220. We describe the x-ray structure of this CR2 domain in complex with C3d at 2.0 angstroms. The structure reveals extensive main chain interactions between C3d and only one short consensus repeat (SCR) of CR2 and substantial SCR side-side packing. These results provide a detailed understanding of receptor-ligand interactions in this protein family and reveal potential target sites for molecular drug design.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Structure at the CR2-C3d interface. (A and B) Surface features of the interface area on C3d (in cyan) and CR2 molecule (in yellow). The shape of the interface of one molecule complements that of the other (prepared using GRASP). (C) Structure of the CR2 SCR2 (yellow) and C3d (cyan) complex. (D and E) The detailed interactions between CR2 (yellow) and C3d (cyan) in two angles. Dashed lines represent H-bonds between carbonyl oxygen atoms (red), nitrogen atoms (blue) of amino acid side chains or main chain, and water molecules (pink). 		Figure 4.
Fig. 4. ELISA results demonstrating the relative inhibition of binding of full-length soluble CR2 at 2 µg/ml to plate-bound C3d by wild-type C3d (wt) compared to mutant C3d (mut1, mut2, and mut4) at several concentrations. Wt and mut1 inhibited CR2-C3d binding similarly, whereas mut2 and mut4 have lost most of their inhibitory capabilities and, thus, do not effectively interact with CR2.
 
  The above figures are reprinted by permission from the AAAs: Science (2001, 292, 1725-1728) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21485028 C.A.Kieslich, D.Morikis, J.Yang, and D.Gunopulos (2011).
Automated computational framework for the analysis of electrostatic similarities of proteins.
  Biotechnol Prog, 27, 316-325.  
21317894 H.P.Morgan, C.Q.Schmidt, M.Guariento, B.S.Blaum, D.Gillespie, A.P.Herbert, D.Kavanagh, H.D.Mertens, D.I.Svergun, C.M.Johansson, D.Uhrín, P.N.Barlow, and J.P.Hannan (2011).
Structural basis for engagement by complement factor H of C3b on a self surface.
  Nat Struct Mol Biol, 18, 463-470.
PDB code: 3oxu
21527715 J.M.van den Elsen, and D.E.Isenman (2011).
A crystal structure of the complex between human complement receptor 2 and its ligand C3d.
  Science, 332, 608-611.
PDB code: 3oed
21397182 P.Mitra, and D.Pal (2011).
Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference.
  Structure, 19, 304-312.  
19835885 C.Q.Schmidt, A.P.Herbert, H.D.Mertens, M.Guariento, D.C.Soares, D.Uhrin, A.J.Rowe, D.I.Svergun, and P.N.Barlow (2010).
The central portion of factor H (modules 10-15) is compact and contains a structurally deviant CCP module.
  J Mol Biol, 395, 105-122.
PDB code: 2kms
20148704 D.Liu, J.Wang, and Z.X.Niu (2010).
Contribution of Chinese Pekin duck complement component C3d-P29 repeats to enhancement of Th2-biased immune responses against NDV F gene induced by DNA immunization.
  Immunopharmacol Immunotoxicol, 32, 297-306.  
19353305 F.Baranyay (2009).
Histochemical contributions to the binding mechanism of complement (CR1, CR2) receptors.
  Pathol Oncol Res, 15, 639-644.  
19164292 J.M.Kovacs, J.P.Hannan, E.Z.Eisenmesser, and V.M.Holers (2009).
Mapping of the C3d ligand binding site on complement receptor 2 (CR2/CD21) using nuclear magnetic resonance and chemical shift analysis.
  J Biol Chem, 284, 9513-9520.  
19605402 S.J.Perkins, A.I.Okemefuna, R.Nan, K.Li, and A.Bonner (2009).
Constrained solution scattering modelling of human antibodies and complement proteins reveals novel biological insights.
  J R Soc Interface, 6, S679-S696.  
19237749 V.Krishnan, Y.Xu, K.Macon, J.E.Volanakis, and S.V.Narayana (2009).
The structure of C2b, a fragment of complement component C2 produced during C3 convertase formation.
  Acta Crystallogr D Biol Crystallogr, 65, 266-274.
PDB code: 3erb
18172655 A.Singh, M.Blank, Y.Shoenfeld, and H.Illges (2008).
Antiphospholipid syndrome patients display reduced titers of soluble CD21 in their sera irrespective of circulating anti-beta2-glycoprotein-I autoantibodies.
  Rheumatol Int, 28, 661-665.  
18400970 D.Liu, J.Y.Zhu, and Z.X.Niu (2008).
Molecular structure and expression of anthropic, ovine, and murine forms of complement receptor type 2.
  Clin Vaccine Immunol, 15, 901-910.  
  19017934 D.Ricklin, S.K.Ricklin-Lichtsteiner, M.M.Markiewski, B.V.Geisbrecht, and J.D.Lambris (2008).
Cutting edge: members of the Staphylococcus aureus extracellular fibrinogen-binding protein family inhibit the interaction of C3d with complement receptor 2.
  J Immunol, 181, 7463-7467.  
18301424 H.J.Gould, and B.J.Sutton (2008).
IgE in allergy and asthma today.
  Nat Rev Immunol, 8, 205-217.  
18786993 K.A.Young, A.P.Herbert, P.N.Barlow, V.M.Holers, and J.P.Hannan (2008).
Molecular basis of the interaction between complement receptor type 2 (CR2/CD21) and Epstein-Barr virus glycoprotein gp350.
  J Virol, 82, 11217-11227.  
18687868 N.Haspel, D.Ricklin, B.V.Geisbrecht, L.E.Kavraki, and J.D.Lambris (2008).
Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d.
  Protein Sci, 17, 1894-1906.
PDB codes: 3d5r 3d5s
17445829 P.Roversi, O.Lissina, S.Johnson, N.Ahmat, G.C.Paesen, K.Ploss, W.Boland, M.A.Nunn, and S.M.Lea (2007).
The structure of OMCI, a novel lipocalin inhibitor of the complement system.
  J Mol Biol, 369, 784-793.
PDB codes: 2cm4 2cm9
17121997 A.W.Serohijos, Y.Chen, F.Ding, T.C.Elston, and N.V.Dokholyan (2006).
A structural model reveals energy transduction in dynein.
  Proc Natl Acad Sci U S A, 103, 18540-18545.
PDB code: 2gf8
17072314 G.Szakonyi, M.G.Klein, J.P.Hannan, K.A.Young, R.Z.Ma, R.Asokan, V.M.Holers, and X.S.Chen (2006).
Structure of the Epstein-Barr virus major envelope glycoprotein.
  Nat Struct Mol Biol, 13, 996.
PDB code: 2h6o
17096529 H.Ding, W.M.Prodinger, and J.Kopecek (2006).
Two-step fluorescence screening of CD21-binding peptides with one-bead one-compound library and investigation of binding properties of N-(2-hydroxypropyl)methacrylamide copolymer-peptide conjugates.
  Biomacromolecules, 7, 3037-3046.  
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.  
16601698 T.S.Jokiranta, V.P.Jaakola, M.J.Lehtinen, M.Pärepalo, S.Meri, and A.Goldman (2006).
Structure of complement factor H carboxyl-terminus reveals molecular basis of atypical haemolytic uremic syndrome.
  EMBO J, 25, 1784-1794.
PDB code: 2g7i
15858010 L.Aldaz-Carroll, J.C.Whitbeck, M.Ponce de Leon, H.Lou, L.Hirao, S.N.Isaacs, B.Moss, R.J.Eisenberg, and G.H.Cohen (2005).
Epitope-mapping studies define two major neutralization sites on the vaccinia virus extracellular enveloped virus glycoprotein B5R.
  J Virol, 79, 6260-6271.  
16172256 R.G.Hibbert, P.Teriete, G.J.Grundy, R.L.Beavil, R.Reljic, V.M.Holers, J.P.Hannan, B.J.Sutton, H.J.Gould, and J.M.McDonnell (2005).
The structure of human CD23 and its interactions with IgE and CD21.
  J Exp Med, 202, 751-760.
PDB codes: 1t8c 1t8d
15486690 C.A.McLure, R.L.Dawkins, J.F.Williamson, R.A.Davies, J.Berry, L.J.Natalie, R.Laird, and S.Gaudieri (2004).
Amino acid patterns within short consensus repeats define conserved duplicons shared by genes of the RCA complex.
  J Mol Evol, 59, 143-157.  
15178763 V.K.Ganesh, S.A.Smith, G.J.Kotwal, and K.H.Murthy (2004).
Structure of vaccinia complement protein in complex with heparin and potential implications for complement regulation.
  Proc Natl Acad Sci U S A, 101, 8924-8929.
PDB code: 1rid
12500981 H.J.Gould, B.J.Sutton, A.J.Beavil, R.L.Beavil, N.McCloskey, H.A.Coker, D.Fear, and L.Smurthwaite (2003).
The biology of IGE and the basis of allergic disease.
  Annu Rev Immunol, 21, 579-628.  
  12813023 H.Song, C.He, C.Knaak, J.M.Guthridge, V.M.Holers, and S.Tomlinson (2003).
Complement receptor 2-mediated targeting of complement inhibitors to sites of complement activation.
  J Clin Invest, 111, 1875-1885.  
12122212 A.E.Prota, D.R.Sage, T.Stehle, and J.D.Fingeroth (2002).
The crystal structure of human CD21: Implications for Epstein-Barr virus and C3d binding.
  Proc Natl Acad Sci U S A, 99, 10641-10646.
PDB code: 1ly2
11955431 B.O.Smith, R.L.Mallin, M.Krych-Goldberg, X.Wang, R.E.Hauhart, K.Bromek, D.Uhrin, J.P.Atkinson, and P.N.Barlow (2002).
Structure of the C3b binding site of CR1 (CD35), the immune adherence receptor.
  Cell, 108, 769-780.
PDB codes: 1gkg 1gkn 1gop
11823416 M.Budayova-Spano, M.Lacroix, N.M.Thielens, G.J.Arlaud, J.C.Fontecilla-Camps, and C.Gaboriaud (2002).
The crystal structure of the zymogen catalytic domain of complement protease C1r reveals that a disruptive mechanical stress is required to trigger activation of the C1 complex.
  EMBO J, 21, 231-239.
PDB code: 1gpz
12421687 M.Krych-Goldberg, J.M.Moulds, and J.P.Atkinson (2002).
Human complement receptor type 1 (CR1) binds to a major malarial adhesin.
  Trends Mol Med, 8, 531-537.  
12501157 R.L.Rich, and D.G.Myszka (2002).
Survey of the year 2001 commercial optical biosensor literature.
  J Mol Recognit, 15, 352-376.  
11728339 S.A.Boackle, V.M.Holers, X.Chen, G.Szakonyi, D.R.Karp, E.K.Wakeland, and L.Morel (2001).
Cr2, a candidate gene in the murine Sle1c lupus susceptibility locus, encodes a dysfunctional protein.
  Immunity, 15, 775-785.  
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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