Crystal structure of unliganded human CD21 SCR1-SCR2 (Complement receptor type 2)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.179 

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The crystal structure of human CD21: Implications for Epstein-Barr virus and C3d binding.

Prota, A.E.Sage, D.R.Stehle, T.Fingeroth, J.D.

(2002) Proc Natl Acad Sci U S A 99: 10641-10646

  • DOI: https://doi.org/10.1073/pnas.162360499
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human complement receptor type 2 (CD21) is the cellular receptor for Epstein-Barr virus (EBV), a human tumor virus. The N-terminal two short consensus repeats (SCR1-SCR2) of the receptor interact with the EBV glycoprotein gp350/220 and also with the natural CD21 ligand C3d. Here we present the crystal structure of the CD21 SCR1-SCR2 fragment in the absence of ligand and demonstrate that it is able to bind EBV. Based on a functional analysis of wild-type and mutant CD21 and molecular modeling, we identify a likely region for EBV attachment and demonstrate that this region is not involved in the interaction with C3d. A comparison with the previously determined structure of CD21 SCR1-SCR2 in complex with C3d shows that, in both cases, CD21 assumes compact V-shaped conformations. However, our analysis reveals a surprising degree of flexibility at the SCR1-SCR2 interface, suggesting interactions between the two domains are not specific. We present evidence that the V-shaped conformation is induced by deglycosylation of the protein, and that physiologic glycosylation of CD21 would result in a more extended conformation, perhaps with additional epitopes for C3d binding.

  • Organizational Affiliation

    Harvard Medical School, Division of Experimental Medicine and Infectious Diseases, Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, 4 Blackfan Circle, Boston, MA 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
complement receptor type 2130Homo sapiensMutation(s): 0 
Gene Names: CR2
UniProt & NIH Common Fund Data Resources
Find proteins for P20023 (Homo sapiens)
Explore P20023 
Go to UniProtKB:  P20023
PHAROS:  P20023
GTEx:  ENSG00000117322 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20023
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.179 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.6α = 91.51
b = 33.27β = 111.44
c = 42.11γ = 117.81
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-05
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary