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- EMDB-2829: The interaction of an essential DNA helicase with RNA polymerase -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-2829
TitleThe interaction of an essential DNA helicase with RNA polymerase
Map dataReconstruction of RNAP-PcrA complex
Sample
  • Sample: RNAP-PcrA complex
  • Protein or peptide: RNAP
  • Protein or peptide: PcrA
KeywordsTranscription / RNA polymerase / helicase
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsHarriott K / Yang X / Mervelet P / Buncherd H / Noirot P / de Jong L / Noirot Gros MF / Lewis PJ
CitationJournal: To Be Published
Title: The interaction of an essential DNA helicase with RNA polymerase
Authors: Harriott K / Yang X / Mervelet P / Buncherd H / Noirot P / de Jong L / Noirot Gros MF / Lewis PJ
History
DepositionNov 28, 2014-
Header (metadata) releaseJan 21, 2015-
Map releaseApr 13, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.52
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.52
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2829.png

Downloads & links

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Map

FileDownload / File: emd_2829.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of RNAP-PcrA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.9 Å/pix.
x 72 pix.
= 280.8 Å		3.9 Å/pix.
x 72 pix.
= 280.8 Å		3.9 Å/pix.
x 72 pix.
= 280.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.52 / Movie #1: 1.52
Minimum - Maximum-2.640136 - 8.35311604
Average (Standard dev.)-0.02571186 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9-9-9
Dimensions727272
Spacing727272
CellA=B=C: 280.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.93.93.9
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-9-9-9
NC/NR/NS727272
D min/max/mean-2.6408.353-0.026

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Supplemental data

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Sample components

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Entire : RNAP-PcrA complex

EntireName: RNAP-PcrA complex
Components
  • Sample: RNAP-PcrA complex
  • Protein or peptide: RNAP
  • Protein or peptide: PcrA

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Supramolecule #1000: RNAP-PcrA complex

SupramoleculeName: RNAP-PcrA complex / type: sample / ID: 1000 / Details: complex was made with in vitro purified proteins / Oligomeric state: 1 / Number unique components: 2
Molecular weightExperimental: 370 KDa / Theoretical: 370 KDa

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Macromolecule #1: RNAP

MacromoleculeName: RNAP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightExperimental: 370 KDa / Theoretical: 370 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: MCC217 / Recombinant plasmid: pSMG69

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Macromolecule #2: PcrA

MacromoleculeName: PcrA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightExperimental: 370 KDa / Theoretical: 370 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: MCC217 / Recombinant plasmid: pSMG69

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.8 / Details: 20 mM Tris, 150 mM NaCl, 10 mM MgCl2, 0.1 mM DTT
StainingType: NEGATIVE
Details: Grids were stained with 1% uranyl formate for 30 seconds
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
DateDec 3, 2008
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 3.9 µm / Number real images: 240 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 14266
Final two d classificationNumber classes: 1178

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