6BDZ

ADAM10 Extracellular Domain Bound by the 11G2 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.cell.2017.11.014
  • Primary Citation of Related Structures:  

  • 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 p ...

    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. Electronic address: stephen_blacklow@hms.harvard.edu.,SBGrid Initiative, Harvard Medical School, Boston, MA 02115, USA.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Cellular Physiology, and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Inserm and Université Paris-Sud, Institut André Lwoff, Villejuif, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
11G2 Fab Light Chain
L
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
11G2 Fab Heavy Chain
H
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Disintegrin and metalloproteinase domain-containing protein 10
A
443Homo sapiensMutation(s): 0 
Gene Names: ADAM10 (KUZ, MADM)
EC: 3.4.24.81
Find proteins for O14672 (Homo sapiens)
Go to Gene View: ADAM10
Go to UniProtKB:  O14672
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.261 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 79.230α = 90.00
b = 97.580β = 90.00
c = 262.720γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-24 
  • Released Date: 2017-12-27 
  • Deposition Author(s): Seegar, T.C.M.

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

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2020-01-01
    Type: Author supporting evidence