6BDZ | pdb_00006bdz

ADAM10 Extracellular Domain Bound by the 11G2 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.317 (Depositor), 0.314 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6BDZ

This is version 3.0 of the entry. See complete history

Literature

Structural Basis for Regulated Proteolysis by the alpha-Secretase ADAM10.

Seegar, T.C.M.Killingsworth, L.B.Saha, N.Meyer, P.A.Patra, D.Zimmerman, B.Janes, P.W.Rubinstein, E.Nikolov, D.B.Skiniotis, G.Kruse, A.C.Blacklow, S.C.

(2017) Cell 171: 1638-1648.e7

  • DOI: https://doi.org/10.1016/j.cell.2017.11.014
  • Primary Citation Related Structures: 
    6BDZ, 6BE6

  • PubMed Abstract: 

    Cleavage of membrane-anchored proteins by ADAM (a disintegrin and metalloproteinase) endopeptidases plays a key role in a wide variety of biological signal transduction and protein turnover processes. Among ADAM family members, ADAM10 stands out as particularly important because it is both responsible for regulated proteolysis of Notch receptors and catalyzes the non-amyloidogenic α-secretase cleavage of the Alzheimer's precursor protein (APP). We present here the X-ray crystal structure of the ADAM10 ectodomain, which, together with biochemical and cellular studies, reveals how access to the enzyme active site is regulated. The enzyme adopts an unanticipated architecture in which the C-terminal cysteine-rich domain partially occludes the enzyme active site, preventing unfettered substrate access. Binding of a modulatory antibody to the cysteine-rich domain liberates the catalytic domain from autoinhibition, enhancing enzymatic activity toward a peptide substrate. Together, these studies reveal a mechanism for regulation of ADAM activity and offer a roadmap for its modulation.


  • Organizational Affiliation
    • Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 98.13 kDa 
  • Atom Count: 6,631 
  • Modeled Residue Count: 855 
  • Deposited Residue Count: 884 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
11G2 Fab Light ChainA [auth L]215Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
11G2 Fab Heavy ChainB [auth H]226Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Disintegrin and metalloproteinase domain-containing protein 10C [auth A]443Homo sapiensMutation(s): 0 
Gene Names: ADAM10KUZMADM
EC: 3.4.24.81
UniProt & NIH Common Fund Data Resources
Find proteins for O14672 (Homo sapiens)
Explore O14672 
Go to UniProtKB:  O14672
PHAROS:  O14672
GTEx:  ENSG00000137845 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14672
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O14672-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G04854NQ
GlyCosmos: G04854NQ
GlyGen: G04854NQ
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO
GlyCosmos: G62182OO
GlyGen: G62182OO

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.317 (Depositor), 0.314 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.23α = 90
b = 97.58β = 90
c = 262.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary