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- EMDB-60131: enteropeptidase with E574A -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-60131
Titleenteropeptidase with E574A
Map data
Sample
  • Complex: E574A mutated enteropeptidase
    • Protein or peptide: Enteropeptidase non-catalytic heavy chain
    • Protein or peptide: Enteropeptidase catalytic light chain
Keywordsmembrane protein
Function / homology
Function and homology information


enteropeptidase / brush border / serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Peptidase S1A, enteropeptidase / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / MAM domain signature. / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SEA domain profile. / SEA domain / SEA domain / SRCR domain profile. ...Peptidase S1A, enteropeptidase / Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / MAM domain signature. / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SEA domain profile. / SEA domain / SEA domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Concanavalin A-like lectin/glucanase domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsSong QY / Ding ZY / Huang HJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of E574A mutated EP at 2.92 angstroms resolution
Authors: Song QY / Ding ZY / Huang HJ
History
DepositionMay 14, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_60131.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.832 Å
Density
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.0017344775 - 2.161598
Average (Standard dev.)0.0014562672 (±0.029574472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 199.68001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : E574A mutated enteropeptidase

EntireName: E574A mutated enteropeptidase
Components
  • Complex: E574A mutated enteropeptidase
    • Protein or peptide: Enteropeptidase non-catalytic heavy chain
    • Protein or peptide: Enteropeptidase catalytic light chain

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Supramolecule #1: E574A mutated enteropeptidase

SupramoleculeName: E574A mutated enteropeptidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Enteropeptidase non-catalytic heavy chain

MacromoleculeName: Enteropeptidase non-catalytic heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.077949 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ICNGSLYPEP TLVPTPPPEL PTDCGGPFEL WEPNTTFSST NFPNSYPNLA FCVWILNAQK GKNIQLHFQE FDLANINDVV EIRDGEEAD SLLLAVYTGP GPVKDVFSTT NRMTVLLITN DVLARGGFKA NFTTGYHLGI PEPCKADHFQ CKNGECVPLV N LCDGHLHC ...String:
ICNGSLYPEP TLVPTPPPEL PTDCGGPFEL WEPNTTFSST NFPNSYPNLA FCVWILNAQK GKNIQLHFQE FDLANINDVV EIRDGEEAD SLLLAVYTGP GPVKDVFSTT NRMTVLLITN DVLARGGFKA NFTTGYHLGI PEPCKADHFQ CKNGECVPLV N LCDGHLHC EDGSDEADCV RFFNGTTNNN GLVRFRIQSI WHTACAENWT TQISNDVCQL LGLGSGNSSK PIFPTDGGPF VK LNTAPDG HLILTPSQQC LQDSLIRLQC NHKSCGKKLA AQDITPK

UniProtKB: Enteropeptidase

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Macromolecule #2: Enteropeptidase catalytic light chain

MacromoleculeName: Enteropeptidase catalytic light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.15068 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IVGGSNAKEG AWPWVVGLYY GGRLLCGASL VSSDWLVSAA ACVYGRNLEP SKWTAILGLH MKSNLTSPQT VPRLIDEIVI NPHYNRRRK DNAIAMMHLE FKVNYTDYIQ PICLPEENQV FPPGRNCSIA GWGTVVYQGT TANILQEADV PLLSNERCQQ Q MPEYNITE ...String:
IVGGSNAKEG AWPWVVGLYY GGRLLCGASL VSSDWLVSAA ACVYGRNLEP SKWTAILGLH MKSNLTSPQT VPRLIDEIVI NPHYNRRRK DNAIAMMHLE FKVNYTDYIQ PICLPEENQV FPPGRNCSIA GWGTVVYQGT TANILQEADV PLLSNERCQQ Q MPEYNITE NMICAGYEEG GIDSCQGDAG GPLMCQENNR WFLAGVTSFG YKCALPNRPG VYARVSRFTE WIQSFLH

UniProtKB: Enteropeptidase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 446564
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

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