8HGG | pdb_00008hgg

Structure of 2:2 PAPP-A.ProMBP complex

• PDB DOI: https://doi.org/10.2210/pdb8HGG/pdb
• EM Map EMD-34738: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2022-11-14 Released: 2023-01-11 
• Deposition Author(s): Zhong, Q.H., Chu, H.L., Wang, G.P., Zhang, C., Wei, Y., Qiao, J., Hang, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the covalent regulation of PAPP-A activity by proMBP and STC2.

Zhong, Q., Chu, H., Wang, G., Zhang, C., Li, R., Guo, F., Meng, X., Lei, X., Zhou, Y., Ren, R., Tao, L., Li, N., Gao, N., Wei, Y., Qiao, J., Hang, J.

(2022) Cell Discov 8: 137-137

• PubMed: 36550107 
• DOI: https://doi.org/10.1038/s41421-022-00502-2
• Primary Citation Related Structures: 
  7Y5N, 7Y5Q, 8HGG, 8HGH


• PubMed Abstract: 
  

  Originally discovered in the circulation of pregnant women as a protein secreted by placental trophoblasts, the metalloprotease pregnancy-associated plasma protein A (PAPP-A) is also widely expressed by many other tissues. It cleaves insulin-like growth factor-binding proteins (IGFBPs) to increase the bioavailability of IGFs and plays essential roles in multiple growth-promoting processes. While the vast majority of the circulatory PAPP-A in pregnancy is proteolytically inactive due to covalent inhibition by proform of eosinophil major basic protein (proMBP), the activity of PAPP-A can also be covalently inhibited by another less characterized modulator, stanniocalcin-2 (STC2). However, the structural basis of PAPP-A proteolysis and the mechanistic differences between these two modulators are poorly understood. Here we present two cryo-EM structures of endogenous purified PAPP-A in complex with either proMBP or STC2. Both modulators form 2:2 heterotetramer with PAPP-A and establish extensive interactions with multiple domains of PAPP-A that are distal to the catalytic cleft. This exosite-binding property results in a steric hindrance to prevent the binding and cleavage of IGFBPs, while the IGFBP linker region-derived peptides harboring the cleavage sites are no longer sensitive to the modulator treatment. Functional investigation into proMBP-mediated PAPP-A regulation in selective intrauterine growth restriction (sIUGR) pregnancy elucidates that PAPP-A and proMBP collaboratively regulate extravillous trophoblast invasion and the consequent fetal growth. Collectively, our work reveals a novel covalent exosite-competitive inhibition mechanism of PAPP-A and its regulatory effect on placental function.

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Organizational Affiliation: 
• Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China.
Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.
National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.
State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China.
Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China.
Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, China.
Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China. [e-mail].
Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China. [e-mail].
Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China. [e-mail].
National Clinical Research Center for Obstetrics and Gynecology, Beijing, China. [e-mail].
Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China. [e-mail].
Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China. [e-mail].
Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China. [e-mail].
National Clinical Research Center for Obstetrics and Gynecology, Beijing, China. [e-mail].
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China. [e-mail].
Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China. [e-mail].
Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, China. [e-mail].
Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China. [e-mail].
National Clinical Research Center for Obstetrics and Gynecology, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 412.96 kDa 
• Atom Count: 25,404 
• Modeled Residue Count: 3,238 
• Deposited Residue Count: 3,698 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone marrow proteoglycan	A, B	222	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13727 (Homo sapiens) Explore P13727  Go to UniProtKB:  P13727
PHAROS:  P13727 GTEx:  ENSG00000186652

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pappalysin-1	C, D	1,627	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth C], F [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Zhong, Q.H., Chu, H.L., Wang, G.P., Zhang, C., Wei, Y., Qiao, J., Hang, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82071658

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary