4EDW

Nerve Growth Factor in Complex with Fab from humanized version of mouse mAb 911 (tanezumab)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Generation of a high-fidelity antibody against nerve growth factor using library scanning mutagenesis and validation with structures of the initial and optimized Fab-antigen complexes.

La Porte, S.L.Eigenbrot, C.Ultsch, M.Ho, W.H.Foletti, D.Forgie, A.Lindquist, K.C.Shelton, D.L.Pons, J.

(null) MAbs 6: 1059-1068

  • DOI: https://doi.org/10.4161/mabs.28677
  • Primary Citation of Related Structures:  
    4EDW, 4EDX

  • PubMed Abstract: 

    Nerve growth factor (NGF) is indispensable during normal embryonic development and critical for the amplification of pain signals in adults. Intervention in NGF signaling holds promise for the alleviation of pain resulting from human diseases such as osteoarthritis, cancer and chronic lower back disorders. We developed a fast, high-fidelity method to convert a hybridoma-derived NGF-targeted mouse antibody into a clinical candidate. This method, termed Library Scanning Mutagenesis (LSM), resulted in the ultra-high affinity antibody tanezumab, a first-in-class anti-hyperalgesic specific for an NGF epitope. Functional and structural comparisons between tanezumab and the mouse 911 precursor antibody using neurotrophin-specific cell survival assays and X-ray crystal structures of both Fab-antigen complexes illustrated high fidelity retention of the NGF epitope. These results suggest the potential for wide applicability of the LSM method for optimization of well-characterized antibodies during humanization.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-nerve growth factorA [auth V]120Homo sapiensMutation(s): 0 
Gene Names: NGFNGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01138 (Homo sapiens)
Explore P01138 
Go to UniProtKB:  P01138
PHAROS:  P01138
GTEx:  ENSG00000134259 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01138
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tanezumab Fab light chainB [auth L]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
tanezumab Fab heavy chainC [auth H]231Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth H]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 92.707β = 90
c = 252.729γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2017-10-25
    Changes: Advisory, Derived calculations, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary