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- EMDB-10186: Structure of the ESX-3 core complex -

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Basic information

Entry
Database: EMDB / ID: EMD-10186
TitleStructure of the ESX-3 core complex
Map data
SampleESX-3 core complex
  • ESX-3 secretion system ATPase EccB3
  • (ESX-3 secretion system protein ...) x 3
Function / homology
Function and homology information


Hydrolases, Acting on acid anhydrides / hydrolase activity / DNA binding / integral component of membrane / ATP binding / plasma membrane
EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 3 domain / FtsK domain profile. / Putative type VII ESX secretion system translocon, EccE / WXG100 protein secretion system (Wss), protein YukD / Type VII secretion system ESX-1, transport TM domain B / FtsK domain / AAA+ ATPase domain / Type VII secretion system membrane protein EccD / Type VII secretion system EccB ...EccCb-like, Actinobacteria / Type VII secretion system EccB, repeat 3 domain / FtsK domain profile. / Putative type VII ESX secretion system translocon, EccE / WXG100 protein secretion system (Wss), protein YukD / Type VII secretion system ESX-1, transport TM domain B / FtsK domain / AAA+ ATPase domain / Type VII secretion system membrane protein EccD / Type VII secretion system EccB / Type VII secretion system protein EccE / EccCa-like, Actinobacteria / FtsK/SpoIIIE family / YukD-like / P-loop containing nucleoside triphosphate hydrolase
ESX-3 secretion system ATPase EccB3 / ESX-3 secretion system protein EccC3 / ESX-3 secretion system protein EccD3 / ESX-3 secretion system protein EccE3
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRivera-Calzada A / Famelis N / Geibel S / Llorca O
Funding support Spain, Germany, 5 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSAF2017-82632-P o-funded by the European Regional Development Fund Spain
European Regional Development FundP2018/NMT4443 co-funded by Autonomous Region of Madrid Spain
European Regional Development FundY2018/BIO4747 co-funded by the Autonomous Region of Madrid Spain
Bavarian State Ministry for Education, Culture, Science and ArtsN-BM-2013-246 Germany
European UnionHorizon 2020, iNEXT (PID2907) , Grant number 653706 Spain
CitationJournal: Nature / Year: 2019
Title: Architecture of the ESX-3/Type VII secretion system
Authors: Famelis N / Rivera-Calzada A / Degliesposti G / Wingender M / Mietrach N / Skehel JM / Fernandez-Leiro R / Bottcher B / Schlosser A / Llorca O / Geibel S
Validation ReportPDB-ID: 6sgw

SummaryFull reportAbout validation report
History
DepositionAug 5, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6sgw
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10186.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 416 pix.
= 442.416 Å
1.06 Å/pix.
x 416 pix.
= 442.416 Å
1.06 Å/pix.
x 416 pix.
= 442.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.086418934 - 0.13493046
Average (Standard dev.)0.00000085145024 (±0.0032126273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 442.41602 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06351.06351.0635
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z442.416442.416442.416
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.0860.1350.000

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Supplemental data

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Sample components

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Entire ESX-3 core complex

EntireName: ESX-3 core 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
Number of components: 5

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Component #1: protein, ESX-3 core complex

ProteinName: ESX-3 core 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
Recombinant expression: No
MassExperimental: 650 kDa
SourceSpecies: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (engineered)Expression System: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Component #2: protein, ESX-3 secretion system ATPase EccB3

ProteinName: ESX-3 secretion system ATPase EccB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 9.407883 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Component #3: protein, ESX-3 secretion system protein EccD3

ProteinName: ESX-3 secretion system protein EccD3 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 47.114125 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Component #4: protein, ESX-3 secretion system protein EccC3

ProteinName: ESX-3 secretion system protein EccC3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.653078 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Component #5: protein, ESX-3 secretion system protein EccE3

ProteinName: ESX-3 secretion system protein EccE3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 30.813355 kDa
SourceSpecies: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155
Source (engineered)Expression System: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / Buffer solution: 30 mM Hepes pH 8.0, 150 mM NaCl / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 % / Details: Blotting time: 3s Blotting force: -10.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1600.0 - 2600.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 11903
Details: Images acquired as 55 frames movies at a calibrated magnification of 1.0635 Angs/px

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 126308 / Details: Images were collected in counting mode
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Map to model correlation coefficient / Refinement space: REAL / Overall bvalue: 76.45
Output model

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