3K2U

Crystal structure of HGFA in complex with the allosteric inhibitory antibody Fab40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Unraveling the allosteric mechanism of serine protease inhibition by an antibody.

Ganesan, R.Eigenbrot, C.Wu, Y.Liang, W.C.Shia, S.Lipari, M.T.Kirchhofer, D.

(2009) Structure 17: 1614-1624

  • DOI: https://doi.org/10.1016/j.str.2009.09.014
  • Primary Citation of Related Structures:  
    2WUB, 2WUC, 3K2U

  • PubMed Abstract: 

    Recent structural studies have outlined the mechanism of protease inhibition by active site-directed antibodies. However, the molecular basis of allosteric inhibition by antibodies has been elusive. Here we report the 2.35 A resolution structure of the trypsin-like serine protease hepatocyte growth factor activator (HGFA) in complex with the allosteric antibody Ab40, a potent inhibitor of HGFA catalytic activity. The antibody binds at the periphery of the substrate binding cleft and imposes a conformational change on the entire 99-loop (chymotrypsinogen numbering). The altered conformation of the 99-loop is incompatible with substrate binding due to the partial collapse of subsite S2 and the reorganization of subsite S4. Remarkably, a single residue deletion of Ab40 abolished inhibition of HGFA activity, commensurate with the reversal of the 99-loop conformation to its "competent" state. The results define an "allosteric switch" mechanism as the basis of protease inhibition by an allosteric antibody.


  • Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor activator long chain257Homo sapiensMutation(s): 0 
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04756 (Homo sapiens)
Explore Q04756 
Go to UniProtKB:  Q04756
PHAROS:  Q04756
GTEx:  ENSG00000109758 
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UniProt GroupQ04756
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q04756-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor activator short chain35Homo sapiensMutation(s): 0 
EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04756 (Homo sapiens)
Explore Q04756 
Go to UniProtKB:  Q04756
PHAROS:  Q04756
GTEx:  ENSG00000109758 
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UniProt GroupQ04756
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody, Fab fragment, Heavy ChainC [auth H]225Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody, Fab fragment, Light ChainD [auth L]214Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.944α = 98.1
b = 48.933β = 95.01
c = 96.034γ = 103.89
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary