[English] 日本語
Yorodumi
- PDB-6sgy: Structure of EccB3 dimer from the ESX-3 core complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sgy
TitleStructure of EccB3 dimer from the ESX-3 core complex
ComponentsESX-3 secretion system protein EccB3
KeywordsMEMBRANE PROTEIN / Type VII Secretion System ESX-3 secretion system T7SS ESX-3 Mycobacterium smegmatis
Function / homologyType 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 / Hydrolases; Acting on acid anhydrides / hydrolase activity / ATP binding / plasma membrane / ESX-3 secretion system ATPase EccB3
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsFamelis, N. / Rivera-Calzada, A. / Llorca, O. / Geibel, S.
Funding support Germany, Spain, 6items
OrganizationGrant numberCountry
German Research FoundationElite Network of Bavaria (N-BM-2013-246), Bavarian State Ministry of Science and the Arts Germany
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P o-funded by the European Regional Development Fund Spain
European Regional Development FundY2018/BIO4747 co-funded by the Autonomous Region of Madrid Spain
European Regional Development FundP2018/NMT4443 co-funded by Autonomous Region of Madrid Spain
European UnionHorizon 2020, iNEXT (PID2907) , Grant number 653706 Spain
Bavarian State Ministry of Science and the Arts Funding OrganisationN-BM-2013-246 Germany
CitationJournal: Nature / Year: 2019
Title: Architecture of the mycobacterial type VII secretion system.
Authors: Nikolaos Famelis / Angel Rivera-Calzada / Gianluca Degliesposti / Maria Wingender / Nicole Mietrach / J Mark Skehel / Rafael Fernandez-Leiro / Bettina Böttcher / Andreas Schlosser / Oscar ...Authors: Nikolaos Famelis / Angel Rivera-Calzada / Gianluca Degliesposti / Maria Wingender / Nicole Mietrach / J Mark Skehel / Rafael Fernandez-Leiro / Bettina Böttcher / Andreas Schlosser / Oscar Llorca / Sebastian Geibel /
Abstract: Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems. A molecular understanding of the ...Host infection by pathogenic mycobacteria, such as Mycobacterium tuberculosis, is facilitated by virulence factors that are secreted by type VII secretion systems. A molecular understanding of the type VII secretion mechanism has been hampered owing to a lack of three-dimensional structures of the fully assembled secretion apparatus. Here we report the cryo-electron microscopy structure of a membrane-embedded core complex of the ESX-3/type VII secretion system from Mycobacterium smegmatis. The core of the ESX-3 secretion machine consists of four protein components-EccB3, EccC3, EccD3 and EccE3, in a 1:1:2:1 stoichiometry-which form two identical protomers. The EccC3 coupling protein comprises a flexible array of four ATPase domains, which are linked to the membrane through a stalk domain. The domain of unknown function (DUF) adjacent to the stalk is identified as an ATPase domain that is essential for secretion. EccB3 is predominantly periplasmatic, but a small segment crosses the membrane and contacts the stalk domain. This suggests that conformational changes in the stalk domain-triggered by substrate binding at the distal end of EccC3 and subsequent ATP hydrolysis in the DUF-could be coupled to substrate secretion to the periplasm. Our results reveal that the architecture of type VII secretion systems differs markedly from that of other known secretion machines, and provide a structural understanding of these systems that will be useful for the design of antimicrobial strategies that target bacterial virulence.
History
DepositionAug 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10188
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESX-3 secretion system protein EccB3
B: ESX-3 secretion system protein EccB3


Theoretical massNumber of molelcules
Total (without water)85,4942
Polymers85,4942
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2460 Å2
ΔGint-11 kcal/mol
Surface area38900 Å2
MethodPISA

-
Components

#1: Protein ESX-3 secretion system protein EccB3 / ESX conserved component B3 / Type VII secretion system protein EccB3 / T7SS protein EccB3


Mass: 42746.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Gene: eccB3, MSMEG_0616, MSMEI_0600
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QQ39

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: EccB3 dimeric structure from ESX-3/Type VII secretion system
Type: COMPLEX
Details: The sample consists of four protein components, EccB3:EccC3:EccD3:EccE3 in a 1:1:2:1 stoichiometry Molecular weight of the complex without the amphipol micelle: 0.65 MDa
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.083 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 8 / Details: 30 mM Hepes pH 8.0, 150 mM NaCl
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: bound to Amphipol A8-35
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K / Details: Blotting time: 3s Blotting force: -10

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 11903
Details: Images acquired as 55 frames movies at a calibrated magnification of 1.0635 Angs/px

-
Processing

EM software
IDNameVersionCategoryDetails
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
7PHENIX1.14model fittingReal-Space Refinement
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIX1.14model refinementMorphing
14UCSF Chimeramodel refinement
Image processingDetails: Images were collected in counting mode
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2066007
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55342
Details: Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the ...Details: Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the EccB3 dimer was subtracted
Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Map correlation coefficient
Details: Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using PHENIX Real-Space Refinement.
Atomic model buildingPDB-ID: 3X3M

3x3m


Pdb chain-ID: A / Pdb chain residue range: 100-518

+
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