[English] 日本語
Yorodumi
- EMDB-9390: Structure of the assembled ATPase EscN from the enteropathogenic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9390
TitleStructure of the assembled ATPase EscN from the enteropathogenic E. coli (EPEC) type III secretion system
Map dataAssembled ATPase EscN from the enteropathogenic E. coli (EPEC) type III secretion system
Sample
  • Complex: Homohexameric complex of ATPase EscN
    • Protein or peptide: Translocator EscN
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: water
KeywordsATPase / Type III Secretion System / ADP / hexamer / HYDROLASE
Function / homology
Function and homology information


protein-secreting ATPase / type III protein secretion system complex / protein secretion by the type III secretion system / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Type 3 secretion system ATPase SCTN / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / : / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities ...Type 3 secretion system ATPase SCTN / ATPase, type III secretion system, FliI/YscN / T3SS EscN ATPase, C-terminal / T3SS EscN ATPase C-terminal domain / : / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
protein-secreting ATPase
Similarity search - Component
Biological speciesEscherichia coli O127:H6 str. E2348/69 (bacteria) / Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsMajewski DD / Worrall LJ
Funding support Canada, United States, 3 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structure of the homohexameric T3SS ATPase-central stalk complex reveals rotary ATPase-like asymmetry.
Authors: Dorothy D Majewski / Liam J Worrall / Chuan Hong / Claire E Atkinson / Marija Vuckovic / Nobuhiko Watanabe / Zhiheng Yu / Natalie C J Strynadka /
Abstract: Many Gram-negative bacteria, including causative agents of dysentery, plague, and typhoid fever, rely on a type III secretion system - a multi-membrane spanning syringe-like apparatus - for their ...Many Gram-negative bacteria, including causative agents of dysentery, plague, and typhoid fever, rely on a type III secretion system - a multi-membrane spanning syringe-like apparatus - for their pathogenicity. The cytosolic ATPase complex of this injectisome is proposed to play an important role in energizing secretion events and substrate recognition. We present the 3.3 Å resolution cryo-EM structure of the enteropathogenic Escherichia coli ATPase EscN in complex with its central stalk EscO. The structure shows an asymmetric pore with different functional states captured in its six catalytic sites, details directly supporting a rotary catalytic mechanism analogous to that of the heterohexameric F/V-ATPases despite its homohexameric nature. Situated at the C-terminal opening of the EscN pore is one molecule of EscO, with primary interaction mediated through an electrostatic interface. The EscN-EscO structure provides significant atomic insights into how the ATPase contributes to type III secretion, including torque generation and binding of chaperone/substrate complexes.
History
DepositionJan 3, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseFeb 20, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6njo
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9390.png

Downloads & links

-
Map

FileDownload / File: emd_9390.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAssembled ATPase EscN from the enteropathogenic E. coli (EPEC) type III secretion system
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 200 pix.
= 204. Å		1.02 Å/pix.
x 200 pix.
= 204. Å		1.02 Å/pix.
x 200 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.15556067 - 0.28870657
Average (Standard dev.)0.0010540612 (±0.009758062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z204.000204.000204.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1560.2890.001

-
Supplemental data

-
Sample components

-
Entire : Homohexameric complex of ATPase EscN

EntireName: Homohexameric complex of ATPase EscN
Components
  • Complex: Homohexameric complex of ATPase EscN
    • Protein or peptide: Translocator EscN
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ALUMINUM FLUORIDE
  • Ligand: water

-
Supramolecule #1: Homohexameric complex of ATPase EscN

SupramoleculeName: Homohexameric complex of ATPase EscN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)

-
Macromolecule #1: Translocator EscN

MacromoleculeName: Translocator EscN / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC
Molecular weightTheoretical: 49.196566 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSHMISEHDS VLEKYPRIQK VLNSTVPALS LNSSTRYEGK IINIGGTIIK ARLPKARIGA FYKIEPSQRL AEVIAIDEDE VFLLPFEHV SGMYCGQWLS YQGDEFKIRV GDALLGRLID GIGRPMESNI VAPYLPFERS LYAEPPDPLL RQVIDQPFIL G VRAIDGLL ...String:
GSHMISEHDS VLEKYPRIQK VLNSTVPALS LNSSTRYEGK IINIGGTIIK ARLPKARIGA FYKIEPSQRL AEVIAIDEDE VFLLPFEHV SGMYCGQWLS YQGDEFKIRV GDALLGRLID GIGRPMESNI VAPYLPFERS LYAEPPDPLL RQVIDQPFIL G VRAIDGLL TCGIGQRIGI FAGSGVGKST LLGMICNGAS ADIIVLALIG ERGREVNEFL ALLPQSTLSK CVLVVTTSDR PA LERMKAA FTATTIAEYF RDQGKNVLLM MDSVTRYARA ARDVGLASGE PDVRGGFPPS VFSSLPKLLE RAGPAPKGSI TAI YTVLLE SDNVNDPIGD EVRSILDGHI VLTRELAEEN HFPAIDIGLS ASRVMHNVVT SEHLRAAAEC KKLIATYKNV ELLI RIGEY TMGQDPEADK AIKNRKLIQN FIQQSTKDIS SYEKTIESLF KVVA

UniProtKB: protein-secreting ATPase

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 4 / Number of copies: 4 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.34 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 600000
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 58000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

2obm

chain_id: A, residue_range: 102-446, source_name: PDB, initial_model_type: experimental model

5b0o

chain_id: A, residue_range: 26-97, source_name: PDB, initial_model_type: experimental model
Detailsphenix.real_space_refine
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6njo:
Structure of the assembled ATPase EscN from the enteropathogenic E. coli (EPEC) type III secretion system

+
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