+Open data
-Basic information
Entry | Database: PDB / ID: 7ufg | ||||||
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Title | Cryo-EM structure of PAPP-A in complex with IGFBP5 | ||||||
Components |
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Keywords | HYDROLASE/Hormone / Metalloprotease / Metal-binding / HYDROLASE / HYDROLASE-Hormone complex | ||||||
Function / homology | Function and homology information negative regulation of muscle tissue development / negative regulation of skeletal muscle hypertrophy / pappalysin-1 / regulation of insulin-like growth factor receptor signaling pathway / response to follicle-stimulating hormone / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of smooth muscle cell migration / mammary gland involution ...negative regulation of muscle tissue development / negative regulation of skeletal muscle hypertrophy / pappalysin-1 / regulation of insulin-like growth factor receptor signaling pathway / response to follicle-stimulating hormone / insulin-like growth factor binding protein complex / insulin-like growth factor ternary complex / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of smooth muscle cell migration / mammary gland involution / negative regulation of growth / insulin-like growth factor II binding / type B pancreatic cell proliferation / insulin-like growth factor I binding / protein metabolic process / positive regulation of vascular associated smooth muscle cell migration / response to growth hormone / positive regulation of insulin-like growth factor receptor signaling pathway / hair follicle morphogenesis / lung alveolus development / response to dexamethasone / fibronectin binding / cellular response to organic cyclic compound / negative regulation of osteoblast differentiation / cellular response to cAMP / positive regulation of vascular associated smooth muscle cell proliferation / striated muscle cell differentiation / negative regulation of cell migration / insulin-like growth factor receptor signaling pathway / female pregnancy / regulation of cell growth / Post-translational protein phosphorylation / negative regulation of smooth muscle cell proliferation / protein catabolic process / metalloendopeptidase activity / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / negative regulation of translation / intracellular signal transduction / endoplasmic reticulum lumen / signal transduction / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | ||||||
Authors | Judge, R.A. / Jain, R. / Hao, Q. / Ouch, C. / Sridar, J. / Smith, C.L. / Wang, J.C.K. / Eaton, D. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of the PAPP-A complex reveals mechanism of substrate recognition. Authors: Russell A Judge / Janani Sridar / Kathryn Tunyasuvunakool / Rinku Jain / John C K Wang / Christna Ouch / Jun Xu / Amirhossein Mafi / Aaron H Nile / Clint Remarcik / Corey L Smith / Crystal ...Authors: Russell A Judge / Janani Sridar / Kathryn Tunyasuvunakool / Rinku Jain / John C K Wang / Christna Ouch / Jun Xu / Amirhossein Mafi / Aaron H Nile / Clint Remarcik / Corey L Smith / Crystal Ghosh / Chen Xu / Vincent Stoll / John Jumper / Amoolya H Singh / Dan Eaton / Qi Hao / Abstract: Insulin-like growth factor (IGF) signaling is highly conserved and tightly regulated by proteases including Pregnancy-Associated Plasma Protein A (PAPP-A). PAPP-A and its paralog PAPP-A2 are ...Insulin-like growth factor (IGF) signaling is highly conserved and tightly regulated by proteases including Pregnancy-Associated Plasma Protein A (PAPP-A). PAPP-A and its paralog PAPP-A2 are metalloproteases that mediate IGF bioavailability through cleavage of IGF binding proteins (IGFBPs). Here, we present single-particle cryo-EM structures of the catalytically inactive mutant PAPP-A (E483A) in complex with a peptide from its substrate IGFBP5 (PAPP-A) and also in its substrate-free form, by leveraging the power of AlphaFold to generate a high quality predicted model as a starting template. We show that PAPP-A is a flexible trans-dimer that binds IGFBP5 via a 25-amino acid anchor peptide which extends into the metalloprotease active site. This unique IGFBP5 anchor peptide that mediates the specific PAPP-A-IGFBP5 interaction is not found in other PAPP-A substrates. Additionally, we illustrate the critical role of the PAPP-A central domain as it mediates both IGFBP5 recognition and trans-dimerization. We further demonstrate that PAPP-A trans-dimer formation and distal inter-domain interactions are both required for efficient proteolysis of IGFBP4, but dispensable for IGFBP5 cleavage. Together the structural and biochemical studies reveal the mechanism of PAPP-A substrate binding and selectivity. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ufg.cif.gz | 728.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ufg.ent.gz | 583.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ufg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ufg_validation.pdf.gz | 416.5 KB | Display | wwPDB validaton report |
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Full document | 7ufg_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 7ufg_validation.xml.gz | 54.9 KB | Display | |
Data in CIF | 7ufg_validation.cif.gz | 88.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/7ufg ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7ufg | HTTPS FTP |
-Related structure data
Related structure data | 26475MC 8d8oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 176341.703 Da / Num. of mol.: 2 / Mutation: E483A, S1144Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAPPA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q13219, pappalysin-1 #2: Protein | Mass: 30876.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGFBP5, IBP5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P24593 #3: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of PAPP-A with IGFBP5 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK 293 |
Buffer solution | pH: 9.2 / Details: BTP (Bis-Tris-Propane) pH 9.2 |
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 47.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9080999 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9080999 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 245018 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.93 Å2 | ||||||||||||||||||||||||
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