2OSL

Crystal structure of Rituximab Fab in complex with an epitope peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Structural basis for recognition of CD20 by therapeutic antibody Rituximab

Du, J., Wang, H., Zhong, C., Peng, B., Zhang, M., Li, B., Huo, S., Guo, Y., Ding, J.

(2007) J Biol Chem 282: 15073-15080

  • DOI: 10.1074/jbc.M701654200
  • Primary Citation of Related Structures:  
    2OSL

  • PubMed Abstract: 

    • Rituximab is a widely used monoclonal antibody drug for treating certain lymphomas and autoimmune diseases. To understand the molecular mechanism of recognition of human CD20 by Rituximab, we determined the crystal structure of the Rituximab Fab in c ...

    Rituximab is a widely used monoclonal antibody drug for treating certain lymphomas and autoimmune diseases. To understand the molecular mechanism of recognition of human CD20 by Rituximab, we determined the crystal structure of the Rituximab Fab in complex with a synthesized peptide comprising the CD20 epitope (residues 163-187) at 2.6-A resolution. The combining site of the Fab consists of four complementarity determining regions that form a large, deep pocket to accommodate the epitope peptide. The bound peptide assumes a unique cyclic conformation that is constrained by a disulfide bond and a rigid proline residue (Pro(172)). The (170)ANPS(173) motif of CD20 is deeply embedded into the pocket on the antibody surface and plays an essential role in the recognition and binding of Rituximab. The antigen-antibody interactions involve both hydrogen bonds and van der Waals contacts and display a high degree of structural and chemical complementarity. These results provide a molecular basis for the specific recognition of CD20 by Rituximab as well as valuable information for development of improved antibody drugs with better specificity and higher affinity.

    Organizational Affiliation: 

    State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
light chain of the Rituximab Fab fragment,light chain of the Rituximab Fab fragmentB, L213Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
heavy chain of the Rituximab Fab fragment,heavy chain of the Rituximab Fab fragmentA, H224Mus musculus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
B-lymphocyte antigen CD20P, Q25Homo sapiensMutation(s): 0 
Gene Names: MS4A1, CD20
Find proteins for P11836 (Homo sapiens)
Explore P11836 
Go to UniProtKB:  P11836
NIH Common Fund Data Resources
PHAROS  P11836
GTEx  ENSG00000156738
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.421α = 90
b = 98.809β = 90
c = 107.241γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2020-01-15
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2020-06-17
    Changes: Data collection, Source and taxonomy