[English] 日本語
Yorodumi
- PDB-9mne: Crystal structure of enteropathogenic Escherichia coli EspC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mne
TitleCrystal structure of enteropathogenic Escherichia coli EspC
ComponentsSerine protease EspC
KeywordsHYDROLASE / Autotransporter protein / Serine protease / Toxins / Bacterial infections / Secretion system / Diarrhoea
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / symbiont-mediated disruption of host tissue / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region
Similarity search - Function
PIC/HAP1/IgA0 second beta-solenoid repeat region / ESPR domain / Extended Signal Peptide of Type V secretion system / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain ...PIC/HAP1/IgA0 second beta-solenoid repeat region / ESPR domain / Extended Signal Peptide of Type V secretion system / Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Serine protease EspC
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsPilapitiya, A.U. / Heras, B. / Paxman, J.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210100673 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1143638 Australia
CitationJournal: Gut Microbes / Year: 2025
Title: The crystal structure of the toxin EspC from enteropathogenic Escherichia coli reveals the mechanism that governs host cell entry and cytotoxicity.
Authors: Pilapitiya, A.U. / Hor, L. / Pan, J. / Wijeyewickrema, L.C. / Pike, R.N. / Leyton, D.L. / Paxman, J.J. / Heras, B.
History
DepositionDec 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Serine protease EspC
A: Serine protease EspC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,04225
Polymers209,4412
Non-polymers2,60123
Water2,810156
1
B: Serine protease EspC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,58516
Polymers104,7211
Non-polymers1,86415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine protease EspC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4579
Polymers104,7211
Non-polymers7378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.469, 94.348, 139.831
Angle α, β, γ (deg.)90.00, 108.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1234-

HOH

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Serine protease EspC


Mass: 104720.664 Da / Num. of mol.: 2 / Fragment: secreted fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (bacteria) / Strain: E2348/69/EPEC / Gene: espC, E2348C_2915 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q9EZE7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Bis-Tris propane (pH 7.4), 0.2 M potassium citrate and 15% (w/v) PEG 3350 and protein at 13 mg/mL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 55473 / % possible obs: 99.1 % / Redundancy: 5.8 % / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.074 / Rrim(I) all: 0.18 / Χ2: 0.597 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.95-3.064.70.8353480.7460.9240.4040.9270.35296.2
3.06-3.185.30.72354790.8220.950.3390.8010.36198.7
3.18-3.325.80.58455440.90.9730.2610.6410.39199.7
3.32-3.55.90.40355610.9460.9860.1790.4420.45499.8
3.5-3.725.90.27655590.9680.9920.1240.3030.49599.7
3.72-45.60.19255540.980.9950.090.2130.57199.5
4-4.4160.13155410.990.9970.0590.1450.70499.4
4.41-5.046.40.09455440.9940.9980.0410.1030.83698.4
5.04-6.356.60.08956290.9950.9990.0380.0970.74599.8
6.35-506.30.04857140.99910.0210.0520.87399.5

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→48.2 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 2919 5.28 %
Rwork0.1628 --
obs0.166 55249 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.94→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14167 0 159 156 14482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.895
X-RAY DIFFRACTIONf_dihedral_angle_d14.0385129
X-RAY DIFFRACTIONf_chiral_restr0.0532218
X-RAY DIFFRACTIONf_plane_restr0.0062586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-2.980.3368880.26831776X-RAY DIFFRACTION69
2.98-3.030.34921310.2592441X-RAY DIFFRACTION96
3.03-3.090.30771300.25082468X-RAY DIFFRACTION97
3.09-3.150.30441340.25572525X-RAY DIFFRACTION98
3.15-3.210.33641340.25172477X-RAY DIFFRACTION99
3.21-3.280.30221460.22682522X-RAY DIFFRACTION99
3.28-3.360.27721430.19342537X-RAY DIFFRACTION99
3.36-3.440.23751350.17032522X-RAY DIFFRACTION99
3.44-3.540.25571360.17192521X-RAY DIFFRACTION99
3.54-3.640.24141360.17142546X-RAY DIFFRACTION99
3.64-3.760.19371320.1762563X-RAY DIFFRACTION100
3.76-3.890.2381570.16572496X-RAY DIFFRACTION99
3.89-4.050.21611350.1422531X-RAY DIFFRACTION99
4.05-4.230.2081340.12832539X-RAY DIFFRACTION100
4.23-4.460.18711860.11142497X-RAY DIFFRACTION99
4.46-4.730.16361520.10592468X-RAY DIFFRACTION98
4.73-5.10.171470.11222558X-RAY DIFFRACTION99
5.1-5.610.18371500.13592543X-RAY DIFFRACTION100
5.61-6.420.2291280.16912588X-RAY DIFFRACTION100
6.42-8.080.2381280.17182602X-RAY DIFFRACTION100
8.09-48.20.19471570.16272610X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3496-0.07260.3081.4042-0.28890.7592-0.1486-0.0526-0.07010.44690.1045-0.03630.0273-0.05260.0430.53750.03840.0490.49040.05520.394441.921-15.428859.8174
20.61370.26330.02031.6563-0.46181.26420.0093-0.05470.01620.38510.0125-0.0131-0.2829-0.1517-0.01060.45650.080.01350.41680.01860.371141.419912.257347.2831
31.39440.3898-0.58041.2249-0.34871.7737-0.05790.1539-0.0334-0.21570.0964-0.2329-0.12430.107-0.0220.486-0.06330.02420.3749-0.02350.452365.97333.87456.3765
40.8398-0.16820.25210.9199-0.12350.69720.04380.0083-0.01630.0558-0.0407-0.136-0.0550.2495-0.03390.6420.0382-0.18780.5383-0.10940.5934102.3401-24.382545.2436
51.2381-0.29030.85460.6065-0.17031.44670.0606-0.1736-0.14960.21740.0683-0.12630.1969-0.0971-0.09910.4585-0.0042-0.06730.3918-0.02030.440577.9359-33.196134.7874
60.5484-0.05060.04481.6012-0.54452.05590.01190.11550.030.0149-0.0147-0.1123-0.25060.0136-0.00180.3872-0.0003-0.01880.4029-0.01170.436669.7699-2.0942-7.4446
71.39390.1989-0.16691.7475-1.00920.6196-0.10830.63430.2902-0.73080.033-0.3221-0.6785-0.05-0.00691.0242-0.02130.05330.75730.09780.638668.431713.6875-30.6385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 54 through 421 )
2X-RAY DIFFRACTION2chain 'B' and (resid 422 through 717 )
3X-RAY DIFFRACTION3chain 'B' and (resid 718 through 1002 )
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 294 )
5X-RAY DIFFRACTION5chain 'A' and (resid 295 through 717 )
6X-RAY DIFFRACTION6chain 'A' and (resid 718 through 913 )
7X-RAY DIFFRACTION7chain 'A' and (resid 914 through 1002 )

+
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