3WD5

Crystal structure of TNFalpha in complex with Adalimumab Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Comparison of the inhibition mechanisms of adalimumab and infliximab in treating tumor necrosis factor alpha-associated diseases from a molecular view

Hu, S.Liang, S.Y.Guo, H.Zhang, D.Li, H.Wang, X.Yang, W.Qian, W.Hou, S.Wang, H.Guo, Y.J.Lou, Z.Y.

(2013) J Biol Chem 288: 27059-27067

  • DOI: 10.1074/jbc.M113.491530
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • TNFα-targeting therapy with the use of the drugs Etanercept, Infliximab, and Adalimumab is used in the clinical treatment of various inflammatory and immune diseases. Although all of these reagents function to disrupt the interaction between TNFα and ...

    TNFα-targeting therapy with the use of the drugs Etanercept, Infliximab, and Adalimumab is used in the clinical treatment of various inflammatory and immune diseases. Although all of these reagents function to disrupt the interaction between TNFα and its receptors, clinical investigations showed the advantages of Adalimumab treatment compared with Etanercept and Infliximab. However, the underlying molecular mechanism of action of Adalimumab remains unclear. In our previous work, we presented structural data on how Infliximab binds with the E-F loop of TNFα and functions as a TNFα receptor-binding blocker. To further elucidate the variations between TNFα inhibitors, we solved the crystal structure of TNFα in complex with Adalimumab Fab. The structural observation and the mutagenesis analysis provided direct evidence for identifying the Adalimumab epitope on TNFα and revealed the mechanism of Adalimumab inhibition of TNFα by occupying the TNFα receptor-binding site. The larger antigen-antibody interface in TNFα Adalimumab also provided information at a molecular level for further understanding the clinical advantages of Adalimumab therapy compared with Infliximab.


    Organizational Affiliation

    From the Laboratory of Structural Biology and Ministry of Education Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing 100084, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factorA157Homo sapiensMutation(s): 0 
Gene Names: TNFATNFTNFSF2
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
NIH Common Fund Data Resources
PHAROS  P01375
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Adalimumab Light ChainL213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Adalimumab Heavy ChainH219Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.849α = 90
b = 161.849β = 90
c = 161.849γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2015-07-01
    Changes: Database references