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- EMDB-1578: Bacillus subtilis RNA polymerase NusA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-1578
TitleBacillus subtilis RNA polymerase NusA complex
Map dataRNAP_NusA complex from Bacillus subtilis
Sample
  • Sample: RNAP_NusA complex
  • Protein or peptide: RNA polymerase
  • Protein or peptide: NusA
KeywordsRNAP NusA Transcription elongation Firmicutes
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsYang X / Molimau S / Doherty GP / Marles-Wright J / Rothnagel R / Hankamer B / Lewis RJ / Lewis PJ
CitationJournal: EMBO Rep / Year: 2009
Title: The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA.
Authors: Xiao Yang / Seeseei Molimau / Geoff P Doherty / Elecia B Johnston / Jon Marles-Wright / Rosalba Rothnagel / Ben Hankamer / Richard J Lewis / Peter J Lewis /
Abstract: There are three stages of transcribing DNA into RNA. These stages are initiation, elongation and termination, and they are well-understood biochemically. However, despite the plethora of structural ...There are three stages of transcribing DNA into RNA. These stages are initiation, elongation and termination, and they are well-understood biochemically. However, despite the plethora of structural information made available on RNA polymerase in the last decade, little is available for RNA polymerase in complex with transcription elongation factors. To understand the mechanisms of transcriptional regulation, we describe the first structure, to our knowledge, for a bacterial RNA polymerase in complex with an essential transcription elongation factor. The resulting structure formed between the RNA polymerase and NusA from Bacillus subtilis provides important insights into the transition from an initiation complex to an elongation complex, and how NusA is able to modulate transcription elongation and termination.
History
DepositionNov 3, 2008-
Header (metadata) releaseNov 5, 2008-
Map releaseAug 17, 2009-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1578.gif

Downloads & links

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Map

FileDownload / File: emd_1578.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNAP_NusA complex from Bacillus subtilis
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 EMDB: 1.95 / Movie #1: 1.9
Minimum - Maximum-5.70949 - 10.3643
Average (Standard dev.)-0.000000000914009 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-36-36-36
Dimensions727272
Spacing727272
CellA=B=C: 280.8 Å
α=β=γ: 90 °

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-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-36-36-36
NC/NR/NS727272
D min/max/mean-5.70910.364-0.000

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Supplemental data

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Sample components

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Entire : RNAP_NusA complex

EntireName: RNAP_NusA complex
Components
  • Sample: RNAP_NusA complex
  • Protein or peptide: RNA polymerase
  • Protein or peptide: NusA

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Supramolecule #1000: RNAP_NusA complex

SupramoleculeName: RNAP_NusA complex / type: sample / ID: 1000 / Details: Monodisperse / Oligomeric state: Dimeric / Number unique components: 2
Molecular weightExperimental: 440 KDa / Theoretical: 440 KDa / Method: Gel filtration

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Macromolecule #1: RNA polymerase

MacromoleculeName: RNA polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: RNAP / Details: Negative staining / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Tissue: Cytoplasm
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa

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Macromolecule #2: NusA

MacromoleculeName: NusA / type: protein_or_peptide / ID: 2 / Name.synonym: NusA / Details: Negative staining / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Tissue: Cytoplasm
Molecular weightExperimental: 40 KDa / Theoretical: 40 KDa

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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

BufferpH: 7.8
Details: 20 mM Tris-HCl pH 7.8, 150 mM NaCl, 10 mM MgCl2, 5% (v/v) glycerol and 1 mM DTT
StainingType: NEGATIVE / Details: 1% Uranyl acetate
GridDetails: Home made carbon
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingDigitization - Sampling interval: 3.9 µm / Number real images: 524 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
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: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 15027

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