+Open data
-Basic information
Entry | Database: PDB / ID: 8h3s | ||||||
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Title | Substrate-bound EP, polyA model | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/HYDROLASE / complex / membrane protein / MEMBRANE PROTEIN-HYDROLASE complex | ||||||
Function / homology | Function and homology information enteropeptidase / Uptake of dietary cobalamins into enterocytes / Activation of Matrix Metalloproteinases / brush border / trypsin / extracellular matrix disassembly / digestion / collagen-containing extracellular matrix / blood microparticle / serine-type endopeptidase activity ...enteropeptidase / Uptake of dietary cobalamins into enterocytes / Activation of Matrix Metalloproteinases / brush border / trypsin / extracellular matrix disassembly / digestion / collagen-containing extracellular matrix / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||
Authors | Ding, Z.Y. / Huang, H.J. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structures reveal the activation and substrate recognition mechanism of human enteropeptidase. Authors: Xiaoli Yang / Zhanyu Ding / Lisi Peng / Qiuyue Song / Deyu Zhang / Fang Cui / Chuanchao Xia / Keliang Li / Hua Yin / Shiyu Li / Zhaoshen Li / Haojie Huang / Abstract: Enteropeptidase (EP) initiates intestinal digestion by proteolytically processing trypsinogen, generating catalytically active trypsin. EP dysfunction causes a series of pancreatic diseases including ...Enteropeptidase (EP) initiates intestinal digestion by proteolytically processing trypsinogen, generating catalytically active trypsin. EP dysfunction causes a series of pancreatic diseases including acute necrotizing pancreatitis. However, the molecular mechanisms of EP activation and substrate recognition remain elusive, due to the lack of structural information on the EP heavy chain. Here, we report cryo-EM structures of human EP in inactive, active, and substrate-bound states at resolutions from 2.7 to 4.9 Å. The EP heavy chain was observed to clamp the light chain with CUB2 domain for substrate recognition. The EP light chain N-terminus induced a rearrangement of surface-loops from inactive to active conformations, resulting in activated EP. The heavy chain then served as a hinge for light-chain conformational changes to recruit and subsequently cleave substrate. Our study provides structural insights into rearrangements of EP surface-loops and heavy chain dynamics in the EP catalytic cycle, advancing our understanding of EP-associated pancreatitis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h3s.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h3s.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 8h3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h3s_validation.pdf.gz | 658.4 KB | Display | wwPDB validaton report |
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Full document | 8h3s_full_validation.pdf.gz | 670.5 KB | Display | |
Data in XML | 8h3s_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 8h3s_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/8h3s ftp://data.pdbj.org/pub/pdb/validation_reports/h3/8h3s | HTTPS FTP |
-Related structure data
Related structure data | 32829MC 7wqwC 7wqxC 7wqzC 7wr7C 8h3uC 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: Antibody | Mass: 66652.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS15, ENTK, PRSS7 / Production host: Homo sapiens (human) / References: UniProt: P98073 |
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#2: Protein | Mass: 26150.680 Da / Num. of mol.: 1 / Mutation: H825A, D876A, S971A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS15, ENTK, PRSS7 / Production host: Homo sapiens (human) / References: UniProt: P98073 |
#3: Protein | Mass: 25042.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Production host: Homo sapiens (human) / References: UniProt: P07477, trypsin |
-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: substrate-bound EP / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 2400 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251202 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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