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- EMDB-3596: The structure of the ESX-5 mycobacterial type VII secretion syste... -

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Basic information

Entry
Database: EMDB / ID: 3596
TitleThe structure of the ESX-5 mycobacterial type VII secretion system membrane complex
SampleESX-5 T7SS membrane complex
SourceMycobacterium xenopi rivm700367 / bacteria
Map data
Methodsingle particle reconstruction, at 13.1 A resolution
AuthorsCiccarelli L / Marlovits TC
CitationNat Microbiol, 2017, 2, 17047-17047

Nat Microbiol, 2017, 2, 17047-17047 StrPapers
Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.
Katherine S H Beckham / Luciano Ciccarelli / Catalin M Bunduc / Haydyn D T Mertens / Roy Ummels / Wolfgang Lugmayr / Julia Mayr / Mandy Rettel / Mikhail M Savitski / Dmitri I Svergun / Wilbert Bitter / Matthias Wilmanns / Thomas C Marlovits / Annabel H A Parret / Edith N G Houben

DateDeposition: Feb 17, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 12, 2017 / Last update: Feb 17, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3596.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
2.18 A/pix
= 697.6 A
320 pix
2.18 A/pix
= 697.6 A
320 pix
2.18 A/pix
= 697.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.18 A
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-1.8008946 - 2.1403747
Average (Standard dev.)0.0028283054 (0.13325706)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 697.60004 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.182.182.18
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z697.600697.600697.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.8012.1400.003

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Supplemental data

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Sample components

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Entire ESX-5 T7SS membrane complex

EntireName: ESX-5 T7SS membrane complex / Details: Solubilized in amphipol A8-35 / Number of components: 1
MassTheoretical: 1.8 MDa

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Component #1: protein, ESX-5 T7SS membrane complex

ProteinName: ESX-5 T7SS membrane complex / Details: Solubilized in amphipol A8-35 / Recombinant expression: No
MassTheoretical: 1.8 MDa
SourceSpecies: Mycobacterium xenopi rivm700367 / bacteria / Strain: RIVM700367
Source (engineered)Expression System: Mycobacterium smegmatis str. mc2 155 / bacteria
Vector: pMV

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 20 mM Tris pH 8, 100 mM NaCl, 5 % (v/v) glycerol
pH: 8
StainingA drop of 2% (w/v) uranyl acetate was added to a carbon-coated grid with absorbed protein and blotted after 30 s.
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 44000 X (calibrated) / Cs: 1.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 5000 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: FEI EAGLE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 65

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C6 (6 fold cyclic) / Number of projections: 1418
3D reconstructionAlgorithm: BACK PROJECTION / Software: EMAN2 / Resolution: 13.1 A / Resolution method: FSC 0.143 CUT-OFF

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