+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32715 | |||||||||
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Title | Structure of Inactive-EP | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information enteropeptidase / brush border / serine-type endopeptidase activity / proteolysis / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Yang XL / Ding ZY / Huang HJ | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32715.map.gz | 33 MB | EMDB map data format | |
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Header (meta data) | emd-32715-v30.xml emd-32715.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd_32715.png | 80 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32715 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32715 | HTTPS FTP |
-Validation report
Summary document | emd_32715_validation.pdf.gz | 389.2 KB | Display | EMDB validaton report |
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Full document | emd_32715_full_validation.pdf.gz | 388.7 KB | Display | |
Data in XML | emd_32715_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_32715_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32715 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32715 | HTTPS FTP |
-Related structure data
Related structure data | 7wqxMC 7wqwC 7wqzC 7wr7C 8h3sC 8h3uC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32715.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.046 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : inactive-EP
Entire | Name: inactive-EP |
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Components |
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-Supramolecule #1: inactive-EP
Supramolecule | Name: inactive-EP / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Enteropeptidase
Macromolecule | Name: Enteropeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: enteropeptidase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.51843 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ELPTDCGGPF ELWEPNTTFS STNFPNSYPN LAFCVWILNA QKGKNIQLHF QEFDLENIND VVEIRDGEEA DSLLLAVYTG PGPVKDVFS TTNRMTVLLI TNDVLARGGF KANFTTGYHL GIPEPCKADH FQCKNGECVP LVNLCDGHLH CEDGSDEADC V RFFNGTTN ...String: ELPTDCGGPF ELWEPNTTFS STNFPNSYPN LAFCVWILNA QKGKNIQLHF QEFDLENIND VVEIRDGEEA DSLLLAVYTG PGPVKDVFS TTNRMTVLLI TNDVLARGGF KANFTTGYHL GIPEPCKADH FQCKNGECVP LVNLCDGHLH CEDGSDEADC V RFFNGTTN NNGLVRFRIQ SIWHTACAEN WTTQISNDVC QLLGLGSGNS SKPIFPTDGG PFVKLNTAPD GHLILTPSQQ CL QDSLIRL QCNHKSCGKK LAAQDITPKI VGGSNAKEGA WPWVVGLYYG GRLLCGASLV SSDWLVSAAH CVYGRNLEPS KWT AILGLH MKSNLTSPQT VPRLIDEIVI NPHYNRRRKD NDIAMMHLEF KVNYTDYIQP ICLPEENQVF PPGRNCSIAG WGTV VYQGT TANILQEADV PLLSNERCQQ QMPEYNITEN MICAGYEEGG IDSCQGDSGG PLMCQENNRW FLAGVTSFGY KCALP NRPG VYARVSRFTE WIQSFLH |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 511658 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: ANGULAR RECONSTITUTION |