[English] 日本語
Yorodumi
- PDB-6umm: A complete structure of the ESX-3 translocon complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6umm
TitleA complete structure of the ESX-3 translocon complex
Components
  • ESX-3 secretion system ATPase EccB3
  • ESX-3 secretion system protein EccC3
  • ESX-3 secretion system protein EccD3
  • ESX-3 secretion system protein EccE3
KeywordsTRANSPORT PROTEIN / ESX / secretion system / type VII secretion system / mycobacteria / complex / membrane protein
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP hydrolysis activity / DNA binding / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain ...Type VII secretion system protein EccE / Putative type VII ESX secretion system translocon, EccE / Type VII secretion system membrane protein EccD / YukD-like / WXG100 protein secretion system (Wss), protein YukD / EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX-3 secretion system ATPase EccB3 / ESX-3 secretion system protein EccC3 / ESX-3 secretion system protein EccD3 / ESX-3 secretion system protein EccE3
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPoweleit, N. / Rosenberg, O.S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1RO1AI128214 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI135990-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PO1AI095208 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI060537 United States
National Institutes of Health/Office of the Director1S10OD021741 United States
CitationJournal: Elife / Year: 2019
Title: The structure of the endogenous ESX-3 secretion system.
Authors: Nicole Poweleit / Nadine Czudnochowski / Rachel Nakagawa / Donovan D Trinidad / Kenan C Murphy / Christopher M Sassetti / Oren S Rosenberg /
Abstract: The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and ...The ESX (or Type VII) secretion systems are protein export systems in mycobacteria and many Gram-positive bacteria that mediate a broad range of functions including virulence, conjugation, and metabolic regulation. These systems translocate folded dimers of WXG100-superfamily protein substrates across the cytoplasmic membrane. We report the cryo-electron microscopy structure of an ESX-3 system, purified using an epitope tag inserted with recombineering into the chromosome of the model organism . The structure reveals a stacked architecture that extends above and below the inner membrane of the bacterium. The ESX-3 protomer complex is assembled from a single copy of the EccB, EccC, and EccE and two copies of the EccD protein. In the structure, the protomers form a stable dimer that is consistent with assembly into a larger oligomer. The ESX-3 structure provides a framework for further study of these important bacterial transporters.
History
DepositionOct 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-20820
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20820
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESX-3 secretion system protein EccE3
B: ESX-3 secretion system protein EccD3
C: ESX-3 secretion system protein EccD3
D: ESX-3 secretion system ATPase EccB3
E: ESX-3 secretion system protein EccC3
F: ESX-3 secretion system protein EccE3
G: ESX-3 secretion system protein EccD3
H: ESX-3 secretion system protein EccD3
I: ESX-3 secretion system ATPase EccB3
J: ESX-3 secretion system protein EccC3


Theoretical massNumber of molelcules
Total (without water)362,88510
Polymers362,88510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ESX-3 secretion system protein EccE3 / ESX conserved component E3 / Type VII secretion system protein EccE3 / T7SS protein EccE3


Mass: 30813.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ48
#2: Protein
ESX-3 secretion system protein EccD3 / ESX conserved component D3 / Type VII secretion system protein EccD3 / T7SS protein EccD3


Mass: 48292.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ46
#3: Protein ESX-3 secretion system ATPase EccB3 / ESX conserved component B3 / Type VII secretion system protein EccB3 / T7SS protein EccB3


Mass: 9145.638 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
References: UniProt: A0QQ39, Hydrolases; Acting on acid anhydrides
#4: Protein ESX-3 secretion system protein EccC3 / ESX conserved component C3 / Type VII secretion system protein EccC3 / T7SS protein EccC3


Mass: 44898.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QQ40

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: ESX-3 translocon complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.66 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Buffer solutionpH: 8
Details: Solutions were made fresh and filter-sterilized before use.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCLC4H11NO31
2150 mMsodium chlorideNaCl1
30.1 %GDNC56H92O251
SpecimenConc.: 5.52 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 73.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 7337

-
Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 778149
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90479 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00624149
ELECTRON MICROSCOPYf_angle_d0.70833117
ELECTRON MICROSCOPYf_dihedral_angle_d13.9414455
ELECTRON MICROSCOPYf_chiral_restr0.0434059
ELECTRON MICROSCOPYf_plane_restr0.0054239

+
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://pdbjlvh1.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