4HIX

Crystal structure of a humanised 3D6 Fab bound to amyloid beta peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bapineuzumab captures the N-terminus of the Alzheimer's disease amyloid-beta peptide in a helical conformation.

Miles, L.A.Crespi, G.A.Doughty, L.Parker, M.W.

(2013) Sci Rep 3: 1302-1302

  • DOI: 10.1038/srep01302
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bapineuzumab is a humanized antibody developed by Pfizer and Johnson & Johnson targeting the amyloid (Aβ) plaques that underlie Alzheimer's disease neuropathology. Here we report the crystal structure of a Fab-Aβ peptide complex that reveals Bapineuz ...

    Bapineuzumab is a humanized antibody developed by Pfizer and Johnson & Johnson targeting the amyloid (Aβ) plaques that underlie Alzheimer's disease neuropathology. Here we report the crystal structure of a Fab-Aβ peptide complex that reveals Bapineuzumab surprisingly captures Aβ in a monomeric helical conformation at the N-terminus. Microscale thermophoresis suggests that the Fab binds soluble Aβ(1-40) with a K(D) of 89 (±9) nM. The structure explains the antibody's exquisite selectivity for particular Aβ species and why it cannot recognize N-terminally modified or truncated Aβ peptides.


    Organizational Affiliation

    ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3056, Australia.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Humanized 3D6 Fab heavy chainH227Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS  P01857
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Humanized 3D6 Fab light chainL220Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: IGKC
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
NIH Common Fund Data Resources
PHAROS  P01834
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Beta-amyloid protein 40A28Homo sapiensMutation(s): 0 
Gene Names: APPA4AD1
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
NIH Common Fund Data Resources
PHAROS  P05067
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.343α = 90
b = 83.039β = 90
c = 91.224γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-03-20
    Changes: Structure summary
  • Version 1.2: 2013-10-02
    Changes: Source and taxonomy
  • Version 1.3: 2014-03-19
    Changes: Source and taxonomy