[English] 日本語
Yorodumi
- EMDB-60121: wtEP-trypsinogen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60121
TitlewtEP-trypsinogen
Map data
Sample
  • Complex: complex of enteropeptidase with trypsinogen
    • Protein or peptide: Serine protease 1
    • Protein or peptide: Enteropeptidase catalytic light chain
    • Protein or peptide: Enteropeptidase non-catalytic heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmembrane protein
Function / homology
Function and homology information


enteropeptidase / Uptake of dietary cobalamins into enterocytes / Developmental Lineage of Pancreatic Acinar Cells / Activation of Matrix Metalloproteinases / brush border / extracellular matrix disassembly / trypsin / digestion / : / blood microparticle ...enteropeptidase / Uptake of dietary cobalamins into enterocytes / Developmental Lineage of Pancreatic Acinar Cells / Activation of Matrix Metalloproteinases / brush border / extracellular matrix disassembly / trypsin / digestion / : / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding / 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
Serine protease 1 / Enteropeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsSong QY / Ding ZY / Huang HJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of trypsinogen-engaged EP at 2.95 angstroms resolution
Authors: Song QY / Ding ZY / Huang HJ
History
DepositionMay 13, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60121.png

Downloads & links

-
Map

FileDownload / File: emd_60121.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 240 pix.
= 223.68 Å		0.93 Å/pix.
x 240 pix.
= 223.68 Å		0.93 Å/pix.
x 240 pix.
= 223.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0017740985 - 2.5398674
Average (Standard dev.)0.0013292611 (±0.026971973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.68 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60121_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60121_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of enteropeptidase with trypsinogen

EntireName: complex of enteropeptidase with trypsinogen
Components
  • Complex: complex of enteropeptidase with trypsinogen
    • Protein or peptide: Serine protease 1
    • Protein or peptide: Enteropeptidase catalytic light chain
    • Protein or peptide: Enteropeptidase non-catalytic heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: complex of enteropeptidase with trypsinogen

SupramoleculeName: complex of enteropeptidase with trypsinogen / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Serine protease 1

MacromoleculeName: Serine protease 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: trypsin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.0421 KDa
SequenceString: APFDDDDKIV GGYNCEENSV PYQVSLNSGY HFCGGSLINE QWVVSAGHCY KSRIQVRLGE HNIEVLEGNE QFINAAKIIR HPQYDRKTL NNDIMLIKLS SRAVINARVS TISLPTAPPA TGTKCLISGW GNTASSGADY PDELQCLDAP VLSQAKCEAS Y PGKITSNM ...String:
APFDDDDKIV GGYNCEENSV PYQVSLNSGY HFCGGSLINE QWVVSAGHCY KSRIQVRLGE HNIEVLEGNE QFINAAKIIR HPQYDRKTL NNDIMLIKLS SRAVINARVS TISLPTAPPA TGTKCLISGW GNTASSGADY PDELQCLDAP VLSQAKCEAS Y PGKITSNM FCVGFLEGGK DSCQGDSGGP VVCNGQLQGV VSWGDGCAQK NKPGVYTKVY NYVKWIKNTI AANS

UniProtKB: Serine protease 1

-
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

-
Macromolecule #3: Enteropeptidase non-catalytic heavy chain

MacromoleculeName: Enteropeptidase non-catalytic heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.766016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IECLPGSSPC TDALTCIKAD LFCDGEVNCP DGSDEDNKMC ATVCDGRFLL TGSSGSFQAT HYPKPSETSV VCQWIIRVNQ GLSIKLSFD DFNTYYTDIL DIYEGVGSSK ILRASIWETN PGTIRIFSNQ VTATFLIESD ESDYVGFNAT YTAFNSSELN N YEKINCNF ...String:
IECLPGSSPC TDALTCIKAD LFCDGEVNCP DGSDEDNKMC ATVCDGRFLL TGSSGSFQAT HYPKPSETSV VCQWIIRVNQ GLSIKLSFD DFNTYYTDIL DIYEGVGSSK ILRASIWETN PGTIRIFSNQ VTATFLIESD ESDYVGFNAT YTAFNSSELN N YEKINCNF EDGFCFWVQD LNDDNEWERI QGSTFSPFTG PNFDHTFGNA SGFYISTPTG PGGRQERVGL LSLPLDPTLE PA CLSFWYH MYGENVHKLS INISNDQNME KTVFQKEGNY GDNWNYGQVT LNETVKFKVA FNAFKNKILS DIALDDISLT YGI CNGSLY PEPTLVPTPP PELPTDCGGP FELWEPNTTF SSTNFPNSYP NLAFCVWILN AQKGKNIQLH FQEFDLENIN DVVE IRDGE EADSLLLAVY TGPGPVKDVF STTNRMTVLL ITNDVLARGG FKANFTTGYH LGIPEPCKAD HFQCKNGECV PLVNL CDGH LHCEDGSDEA DCVRFFNGTT NNNGLVRFRI QSIWHTACAE NWTTQISNDV CQLLGLGSGN SSKPIFPTDG GPFVKL NTA PDGHLILTPS QQCLQDSLIR LQCNHKSCGK KLAAQDITPK

UniProtKB: Enteropeptidase

-
Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 311357
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more