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 8SL1 | pdb_00008sl1

Cryo-EM structure of PAPP-A2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Cryo-EM structure of human PAPP-A2 and mechanism of substrate recognition.

Sridar, J., Mafi, A., Judge, R.A., Xu, J., Kong, K.A., Wang, J.C.K., Stoll, V.S., Koukos, G., Simon, R.J., Eaton, D., Bratkowski, M., Hao, Q.

(2023) Commun Chem 6: 234-234

  • DOI: https://doi.org/10.1038/s42004-023-01032-y
  • Primary Citation Related Structures: 
    8SL1

  • PubMed Abstract: 

    Pregnancy-Associated Plasma Protein A isoforms, PAPP-A and PAPP-A2, are metalloproteases that cleave insulin-like growth factor binding proteins (IGFBPs) to modulate insulin-like growth factor signaling. The structures of homodimeric PAPP-A in complex with IGFBP5 anchor peptide, and inhibitor proteins STC2 and proMBP have been recently reported. Here, we present the single-particle cryo-EM structure of the monomeric, N-terminal LG, MP, and the M1 domains (with the exception of LNR1/2) of human PAPP-A2 to 3.13 Å resolution. Our structure together with functional studies provides insight into a previously reported patient mutation that inactivates PAPP-A2 in a distal region of the protein. Using a combinational approach, we suggest that PAPP-A2 recognizes IGFBP5 in a similar manner as PAPP-A and show that PAPP-A2 cleaves IGFBP5 less efficiently due to differences in the M2 domain. Overall, our studies characterize the cleavage mechanism of IGFBP5 by PAPP-A2 and shed light onto key differences with its paralog PAPP-A.


  • Organizational Affiliation: 
    • Calico Life Sciences LLC, South San Francisco, CA, 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 175.05 kDa 
  • Atom Count: 6,608 
  • Modeled Residue Count: 843 
  • Deposited Residue Count: 1,570 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pappalysin-21,570Homo sapiensMutation(s): 0 
Gene Names: PAPPA2, PLAC3
EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXP8 (Homo sapiens)
Explore Q9BXP8 
Go to UniProtKB:  Q9BXP8
PHAROS:  Q9BXP8
GTEx:  ENSG00000116183 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXP8
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9BXP8-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-05-14
    Changes: Data collection