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- EMDB-9747: Type VI secretion system membrane core complex -

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Basic information

Entry
Database: EMDB / ID: 9747
TitleType VI secretion system membrane core complexType VI secretion system
Map dataT6SS membrane core complex
SampleType VI Secretion System membrane core complex TssJLMType VI secretion system:
(Type VI Secretion System ...) x 2
Function / homologyIcmF-related / Type VI secretion system IcmF, C-terminal / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion protein IcmF C-terminal / Intracellular multiplication and human macrophage-killing / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / integral component of membrane / Uncharacterized protein / Uncharacterized protein
Function and homology information
SourceEscherichia coli 55989 (bacteria) / Escherichia coli (strain 55989 / EAEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsYin M / Yan Z
CitationJournal: Cell Res. / Year: 2019
Title: Architecture of type VI secretion system membrane core complex.
Authors: Meng Yin / Zhaofeng Yan / Xueming Li
Validation ReportPDB-ID: 6ixh

SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Jan 30, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Map surface with fitted models
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ixh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9747.map.gz (map file in CCP4 format, 157217 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
340 pix
1.32 Å/pix.
= 448.8 Å
340 pix
1.32 Å/pix.
= 448.8 Å
340 pix
1.32 Å/pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.13804519 - 0.22493486
Average (Standard dev.)0.0007299888 (0.005843512)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions340340340
Origin0.00.00.0
Limit339.0339.0339.0
Spacing340340340
CellA=B=C: 448.80002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z448.800448.800448.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.1380.2250.001

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Supplemental data

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Sample components

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Entire Type VI Secretion System membrane core complex TssJLM

EntireName: Type VI Secretion System membrane core complex TssJLM / Number of components: 3

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Component #1: protein, Type VI Secretion System membrane core complex TssJLM

ProteinName: Type VI Secretion System membrane core complex TssJLMType VI secretion system
Recombinant expression: No
SourceSpecies: Escherichia coli 55989 (bacteria) / Strain: 55989
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)

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Component #2: protein, Type VI Secretion System TssJ

ProteinName: Type VI Secretion System TssJType VI secretion system / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 19.27109 kDa
SourceSpecies: Escherichia coli (strain 55989 / EAEC) (bacteria) / Strain: 55989 / EAEC
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, Type VI Secretion System TssM

ProteinName: Type VI Secretion System TssMType VI secretion system / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 127.11307 kDa
SourceSpecies: Escherichia coli (strain 55989 / EAEC) (bacteria) / Strain: 55989 / EAEC
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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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: 5 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 44069
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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