3EOB | pdb_00003eob

Crystal structure the Fab fragment of Efalizumab in complex with LFA-1 I domain, Form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.333 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.269 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3EOB

This is version 1.2 of the entry. See complete history

Literature

Efalizumab binding to the LFA-1 alphaL I domain blocks ICAM-1 binding via steric hindrance.

Li, S.Wang, H.Peng, B.Zhang, M.Zhang, D.Hou, S.Guo, Y.Ding, J.

(2009) Proc Natl Acad Sci U S A 106: 4349-4354

  • DOI: https://doi.org/10.1073/pnas.0810844106
  • Primary Citation Related Structures: 
    3EO9, 3EOA, 3EOB

  • PubMed Abstract: 

    Lymphocyte function-associated antigen 1 (LFA-1) plays important roles in immune cell adhesion, trafficking, and activation and is a therapeutic target for the treatment of multiple autoimmune diseases. Efalizumab is one of the most efficacious antibody drugs for treating psoriasis, a very common skin disease, through inhibition of the binding of LFA-1 to the ligand intercellular adhesion molecule 1 (ICAM-1). We report here the crystal structures of the Efalizumab Fab alone and in complex with the LFA-1 alpha(L) I domain, which reveal the molecular mechanism of inhibition of LFA-1 by Efalizumab. The Fab binds with an epitope on the inserted (I) domain that is distinct from the ligand-binding site. Efalizumab binding blocks the binding of LFA-1 to ICAM-1 via steric hindrance between its light chain and ICAM-1 domain 2 and thus inhibits the activities of LFA-1. These results have important implications for the development of improved antibodies and new therapeutic strategies for the treatment of autoimmune diseases.


  • Organizational Affiliation
    • State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Macromolecule Content 

  • Total Structure Weight: 135.86 kDa 
  • Atom Count: 9,454 
  • Modeled Residue Count: 1,216 
  • Deposited Residue Count: 1,230 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Efalizumab Fab fragment, light chainA [auth L],
D [auth A]
214Homo sapiensMutation(s): 0 
Gene Names: IGG1
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Efalizumab Fab fragment, heavy chainB [auth H],
E [auth B]
220Homo sapiensMutation(s): 0 
Gene Names: IGG1
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-LC [auth I],
F [auth J]
181Homo sapiensMutation(s): 0 
Gene Names: LFA-1 I domain
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens)
Explore P20701 
Go to UniProtKB:  P20701
PHAROS:  P20701
GTEx:  ENSG00000005844 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20701
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.333 (Depositor), 0.330 (DCC) 
  • R-Value Work:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.269 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.096α = 90
b = 111.096β = 90
c = 470.726γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary