8A7E

PAPP-A dimer in complex with its inhibitor STC2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the proteolytic enzyme PAPP-A with the endogenous inhibitor stanniocalcin-2 reveals its inhibitory mechanism.

Kobbero, S.D.Gajhede, M.Mirza, O.A.Kloverpris, S.Kjaer, T.R.Mikkelsen, J.H.Boesen, T.Oxvig, C.

(2022) Nat Commun 13: 6084-6084

  • DOI: https://doi.org/10.1038/s41467-022-33698-8
  • Primary Citation of Related Structures:  
    8A7D, 8A7E

  • PubMed Abstract: 

    The metzincin metalloproteinase PAPP-A plays a key role in the regulation of insulin-like growth factor (IGF) signaling by specific cleavage of inhibitory IGF binding proteins (IGFBPs). Using single-particle cryo-electron microscopy (cryo-EM), we here report the structure of PAPP-A in complex with its endogenous inhibitor, stanniocalcin-2 (STC2), neither of which have been reported before. The highest resolution (3.1 Å) was obtained for the STC2 subunit and the N-terminal approximately 1000 residues of the PAPP-A subunit. The 500 kDa 2:2 PAPP-A·STC2 complex is a flexible multidomain ensemble with numerous interdomain contacts. In particular, a specific disulfide bond between the subunits of STC2 and PAPP-A prevents dissociation, and interactions between STC2 and a module located in the very C-terminal end of the PAPP-A subunit prevent binding of its main substrate, IGFBP-4. While devoid of activity towards IGFBP-4, the active site cleft of the catalytic domain is accessible in the inhibited PAPP-A·STC2 complex, as shown by its ability to hydrolyze a synthetic peptide derived from IGFBP-4. Relevant to multiple human pathologies, this unusual mechanism of proteolytic inhibition may support the development of specific pharmaceutical agents, by which IGF signaling can be indirectly modulated.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus C, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stanniocalcin-2A [auth P],
C [auth A]
168Homo sapiensMutation(s): 0 
Gene Names: STC2
UniProt & NIH Common Fund Data Resources
Find proteins for O76061 (Homo sapiens)
Explore O76061 
Go to UniProtKB:  O76061
PHAROS:  O76061
GTEx:  ENSG00000113739 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76061
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pappalysin-1B [auth C],
D [auth Q]
1,536Homo sapiensMutation(s): 1 
Gene Names: PAPPA
EC: 3.4.24.79
UniProt & NIH Common Fund Data Resources
Find proteins for Q13219 (Homo sapiens)
Explore Q13219 
Go to UniProtKB:  Q13219
PHAROS:  Q13219
GTEx:  ENSG00000182752 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13219
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth C],
N [auth Q]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
H [auth C]
I [auth C]
J [auth C]
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth C],
O [auth Q],
P [auth Q],
Q,
R [auth Q],
S [auth Q],
T [auth Q],
U [auth Q],
V [auth Q]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONPHENIX1.20
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary