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- EMDB-12674: Map of the hexameric ESX-5 complex from Mycobacterium xenopi with... -

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Basic information

Entry
Database: EMDB / ID: EMD-12674
TitleMap of the hexameric ESX-5 complex from Mycobacterium xenopi with periplasmic region
Map dataMap of a hexameric ESX-5 complex from Mycobacterium xenopi with periplasmic region
Sample
  • Complex: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
Function / homology
Function and homology information


hydrolase activity / ATP hydrolysis activity / DNA binding / ATP binding / membrane / 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
Secretion protein Snm4 / Type VII secretion protein EccE / Type VII secretion protein EccB / FtsK domain-containing protein
Similarity search - Component
Biological speciesMycobacterium xenopi RIVM700367 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsRitter C / Chojnowski G / Beckham KSH / Mullapudi E / Rettel M / Savitski MM / Mortensen SA / Ziemianowicz D / Kosinski J / Wilmanns M
CitationJournal: Sci Adv / Year: 2021
Title: Structure of the mycobacterial ESX-5 type VII secretion system pore complex.
Authors: Katherine S H Beckham / Christina Ritter / Grzegorz Chojnowski / Daniel S Ziemianowicz / Edukondalu Mullapudi / Mandy Rettel / Mikhail M Savitski / Simon A Mortensen / Jan Kosinski / Matthias Wilmanns /
Abstract: The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation ...The ESX-5 type VII secretion system is a membrane-spanning protein complex key to the virulence of mycobacterial pathogens. However, the overall architecture of the fully assembled translocation machinery and the composition of the central secretion pore have remained unknown. Here, we present the high-resolution structure of the 2.1-megadalton ESX-5 core complex. Our structure captured a dynamic, secretion-competent conformation of the pore within a well-defined transmembrane section, sandwiched between two flexible protein layers at the cytosolic entrance and the periplasmic exit. We propose that this flexibility endows the ESX-5 machinery with large conformational plasticity required to accommodate targeted protein secretion. Compared to known secretion systems, a highly dynamic state of the pore may represent a fundamental principle of bacterial secretion machineries.
History
DepositionMar 26, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12674.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of a hexameric ESX-5 complex from Mycobacterium xenopi with periplasmic region
Voxel sizeX=Y=Z: 1.29 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.12815419 - 0.36020666
Average (Standard dev.)0.0007071969 (±0.013197774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9-9-9
Dimensions468468468
Spacing468468468
CellA=B=C: 603.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.291.291.29
M x/y/z468468468
origin x/y/z0.0000.0000.000
length x/y/z603.720603.720603.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-9-9-9
NC/NR/NS468468468
D min/max/mean-0.1280.3600.001

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Supplemental data

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Sample components

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Entire : Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...

EntireName: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
Components
  • Complex: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE

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Supramolecule #1: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, ...

SupramoleculeName: Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycobacterium xenopi RIVM700367 (bacteria) / Location in cell: membrane
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 2.142 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationName
20.0 mMTris pH 8.0
150.0 mMNaClSodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 nm
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -0.7000000000000001 µm / Nominal defocus min: -1.7 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 27873 / Average electron dose: 49.34 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 2.14)
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.14)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14) / Number images used: 52015

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