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- EMDB-2136: Negative stain EM composite structure (part 1) of the type IV sec... -

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Basic information

Entry
Database: EMDB / ID: 2136
TitleNegative stain EM composite structure (part 1) of the type IV secretion system subcomplex VirB4-VirB7-VirB9-VirB10
SampleTraB/TraN/TraO/TraF complex encoded by pKM101
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataCore complex part of the VirB4-core complex composite reconstruction
Methodsingle particle reconstruction, at 20 A resolution
AuthorsWilliams R / Wallden K / Yan J / Lian PW / Wang L / Thalassinos K / Orlova EV / Waksman G
CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 11348-11353

Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 11348-11353 StrPapers
Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.
Karin Walldén / Robert Williams / Jun Yan / Pei W Lian / Luchun Wang / Konstantinos Thalassinos / Elena V Orlova / Gabriel Waksman

DateDeposition: Jun 12, 2012 / Header (metadata) release: Jul 25, 2012 / Map release: Aug 1, 2012 / Last update: Jun 12, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Slabnear <=> far

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Supplemental images

Downloads & links

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Map

Fileemd_2136.map.gz (map file in CCP4 format, 61037 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.67 A/pix
= 417.5 A
250 pix
1.67 A/pix
= 417.5 A
250 pix
1.67 A/pix
= 417.5 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.67 A
Density
Contour Level:0.35 (by emdb), 0.25 (movie #1):
Minimum - Maximum-1.48925638 - 1.98086631
Average (Standard dev.)0.0111697 (0.09054922)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin-125-125-125
Limit124124124
Spacing250250250
CellA=B=C: 417.5 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.671.671.67
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z417.500417.500417.500
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-125-125-125
NC/NR/NS250250250
D min/max/mean-1.4891.9810.011

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Supplemental data

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Sample components

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Entire TraB/TraN/TraO/TraF complex encoded by pKM101

EntireName: TraB/TraN/TraO/TraF complex encoded by pKM101 / Number of components: 4
Oligomeric State: 14-mer of core complex (TraN/TraO/TraF) and monomer of TraB
MassTheoretical: 1.15 MDa / Experimental: 1.15 MDa

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Component #1: protein, TraB

ProteinName: TraB / a.k.a: VirB4
Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies: 1 / Recombinant expression: Yes
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: pKM101 plasmid
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK IBA3C
Source (natural)Location in cell: cell envelope

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Component #2: protein, TraN

ProteinName: TraN / a.k.a: VirB7
Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Recombinant expression: Yes / Number of Copies: 14
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: pKM101 plasmid
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK IBA3C
Source (natural)Location in cell: cell envelope

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Component #3: protein, TraO

ProteinName: TraO / a.k.a: VirB9
Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Number of Copies: 14 / Recombinant expression: Yes
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: pKM101 plasmid
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK IBA3C
Source (natural)Location in cell: cell envelope

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Component #4: protein, TraF

ProteinName: TraF / a.k.a: VirB10
Details: The 1.05 MDa core complex (TraN/TraO/TraF) with TraB bound, see EMD-2137
Recombinant expression: Yes / Number of Copies: 14
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: pKM101 plasmid
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pASK IBA3C
Source (natural)Location in cell: cell envelope

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Experimental details

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Sample preparation

Specimen stateparticle
Support filmGlow-discharged continuous carbon
StainingNanoW
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Dec 22, 2009
Electron gunElectron source: OTHER / Accelerating voltage: 120 kV / Illumination mode: SPOT SCAN
LensMagnification: 42000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 2000 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: GENERIC FILM

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Image acquisition

Image acquisitionNumber of digital images: 12 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 330 / Number of projections: 10000 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Common lines / Software: IMAGIC
Details: This map is part of a composite structure of two maps.
Resolution: 20 A / Resolution method: FSC 0.5

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