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- EMDB-3568: 3D reconstruction for the thin CcdA-CcdB-DNA filaments based on t... -

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Basic information

Entry
Database: EMDB / ID: 3568
Title3D reconstruction for the thin CcdA-CcdB-DNA filaments based on the negative stain electron microscopy dataset.
SampleThin filaments formed as the complex between DNA, antitoxin CcdA and toxin CcdB.
SourceEscherichia coli k-12 / bacteria / image: Escherichia coli
Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map data3D reconstruction for the thin CcdA-CcdB-DNA filaments based on the negative stain electron microscopy dataset.
Methodhelical reconstruction, at 23 A resolution
AuthorsVandervelde A / Efremov R / Loris R
CitationNucleic Acids Res., 2017

Nucleic Acids Res., 2017 StrPapers
Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon.
Alexandra Vandervelde / Igor Drobnak / San Hadži / Yann G-J Sterckx / Thomas Welte / Henri De Greve / Daniel Charlier / Rouslan Efremov / Remy Loris / Jurij Lah

DateDeposition: Jan 12, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: Mar 1, 2017 / Last update: Jan 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3568.map.gz (map file in CCP4 format, 2917 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
4.58 A/pix
= 412.2 A
90 pix
4.58 A/pix
= 412.2 A
90 pix
4.58 A/pix
= 412.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.58 A
Density
Contour Level:0.0421 (by author), 0.015 (movie #1):
Minimum - Maximum-0.02525345 - 0.15503567
Average (Standard dev.)-0.00061731157 (0.009161664)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions909090
Origin-45-45-45
Limit444444
Spacing909090
CellA=B=C: 412.19998 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.584.584.58
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z412.200412.200412.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-45-45-45
NC/NR/NS909090
D min/max/mean-0.0250.155-0.001

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Supplemental data

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Sample components

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Entire Thin filaments formed as the complex between DNA, antitoxin CcdA ...

EntireName: Thin filaments formed as the complex between DNA, antitoxin CcdA and toxin CcdB.
Number of components: 6

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Component #1: protein, Thin filaments formed as the complex between DNA, antito...

ProteinName: Thin filaments formed as the complex between DNA, antitoxin CcdA and toxin CcdB.
Recombinant expression: No

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Component #2: protein, antitoxin CcdA and toxin CcdB

ProteinName: antitoxin CcdA and toxin CcdB / Recombinant expression: No
SourceSpecies: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Synthetic construct

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Component #4: protein, Antitoxin CcdA

ProteinName: Antitoxin CcdA / Recombinant expression: No
Source (engineered)Expression System: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #5: protein, Toxin CcdB

ProteinName: Toxin CcdB / Recombinant expression: No
Source (engineered)Expression System: Escherichia coli k-12 / bacteria / image: Escherichia coli

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Component #6: nucleic-acid, DNA

Nucleic-acidName: DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
AATTGTGATG CTTCTAAAAT TACTAAAATT GAGGATTTTA ATGCTACAAC AATGCCTGCC TCTTCTTATT TCTCCGGAGA TCCGAAAACC CCAAGTTACG GATCTTCCTC TCCCTCCGCA CAGCGTTACA TCCCGTCAGC ACAGCATGTA GTGCCTCATA CAGTTGCCCA TGGCACTATA TGTTGTGTTG TATCTCTGGA CTGTGATGCG CCGCGCAGGG GCGGAAAACA GCGATATGAT GATTTTCTCA GCGTTGTACA CTTCCGGAAA GTCGTTTATT CAAATAAAGT CGGATCCATA CGAAACGGGA ATGCGGTAAT TACGCTTTGT TTTTATAAGT CAGATTTTAA TTTTTATTGG TTAACATAAC GAAAGGTAAA ATACATAAGG CTTACTAAAA GCCAGATAAC AGTATGCGTA TTTGCGCGCT GATTTTTGCG GTATAAGAAT ATATACTGAT ATGTATACCC GAAGTATGTC AAAAAGAGGT GTGCTATGAA GCAGCGTATT ACAGTGACAG TTGACAGCGA CAGCTATCAG TTGCTCAAGG CATATGATGT CAATATCTCC GGTCTGGTAA GCACAACCAT GCAGAATGAA GCCCGTCGTC TGCGTGCCGA ACGCTGGAAA GCGGAAAATC AGGAAGGGAT GGCTGAGGTC GCCCGGTTTA TTGAAATGAA CGGCTCTTTT GCTGACGAGA ACAGGGACTG GTGAAATGCA GTTTAAGGTT TACACCTATA AAAGAGAGAG CCGTTATCGT CTGTTTGTGG ATGTACAGAG TGATATTATT GACACGCCCG GGCGACGGAT GGTGATCCCC CTGGCCAGTG CACGTCTGCT GTCAGATAAA GTCTCCCGTG AACTTTACCC GGTGGTGCAT ATCGGGGATG AAAGCTGGCG CATGATGACC ACCGATATGG CCAGTGTGCC GGTCTCCGTT ATCGGGGAAG AAGTGGCTGA TCTCAGCCAC CGCGAAAATG ACATCAAAAA CGCCATTAAC C

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 38.4 A / Delta phi: 64.3 deg.
Sample solutionBuffer solution: Just before staining, the sample was supplemented with 5 mM MgAc2 (final concentration).
pH: 7.5
Support filmELMO glow discharger
StainingThe sample was applied to a freshly glow-discharged grid for five minutes after which the grid was washed with 5 mM MgAc2 and adsorbed protein stained with 1% uranyl formate.
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 1400
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 50 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 3.4 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 2500 nm
Specimen HolderModel: JEOL
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 358

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPARX / Resolution: 23 A / Resolution method: FSC 0.5 CUT-OFF
FSC plot (resolution assessment)

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