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- EMDB-1218: The structural basis for regulated assembly and function of the t... -

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Basic information

Entry
Database: EMDB / ID: EMD-1218
TitleThe structural basis for regulated assembly and function of the transcriptional activator NtrC.
Map data3D map of full-length, BeF-activated NtrC in the ADP-AlF state
Sample
  • Sample: Full length, active NtrC
  • Protein or peptide: Transcription activator
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsDe Carlo S / Chen B / Hoover TR / Kondrashkina E / Nogales E / Nixon BT
CitationJournal: Genes Dev / Year: 2006
Title: The structural basis for regulated assembly and function of the transcriptional activator NtrC.
Authors: Sacha De Carlo / Baoyu Chen / Timothy R Hoover / Elena Kondrashkina / Eva Nogales / B Tracy Nixon /
Abstract: In two-component signal transduction, an input triggers phosphorylation of receiver domains that regulate the status of output modules. One such module is the AAA+ ATPase domain in bacterial enhancer- ...In two-component signal transduction, an input triggers phosphorylation of receiver domains that regulate the status of output modules. One such module is the AAA+ ATPase domain in bacterial enhancer-binding proteins that remodel the sigma(54) form of RNA polymerase. We report X-ray solution scattering and electron microscopy structures of the activated, full-length nitrogen-regulatory protein C (NtrC) showing a novel mechanism for regulation of AAA+ ATPase assembly via the juxtaposition of the receiver domains and ATPase ring. Accompanying the hydrolysis cycle that is required for transcriptional activation, we observed major order-disorder changes in the GAFTGA loops involved in sigma(54) binding, as well as in the DNA-binding domains.
History
DepositionMar 22, 2006-
Header (metadata) releaseApr 24, 2006-
Map releaseApr 24, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.000363
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.000363
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1218.gif

Downloads & links

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Map

FileDownload / File: emd_1218.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of full-length, BeF-activated NtrC in the ADP-AlF state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.56 Å/pix.
x 125 pix.
= 320. Å		2.56 Å/pix.
x 125 pix.
= 320. Å		2.56 Å/pix.
x 125 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.56 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.000107 / Movie #1: 0.000363
Minimum - Maximum-0.00149751 - 0.0013223
Average (Standard dev.)0.0000280043 (±0.0000793012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions125125125
Spacing125125125
CellA=B=C: 320 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.562.562.56
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS125125125
D min/max/mean-0.0010.0010.000

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Supplemental data

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Sample components

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Entire : Full length, active NtrC

EntireName: Full length, active NtrC
Components
  • Sample: Full length, active NtrC
  • Protein or peptide: Transcription activator

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Supramolecule #1000: Full length, active NtrC

SupramoleculeName: Full length, active NtrC / type: sample / ID: 1000 / Details: Activated with Mg/BeF / Oligomeric state: Hexamer / Number unique components: 1
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa / Method: Sedimentation Velocity, Analytical centrifugation

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Macromolecule #1: Transcription activator

MacromoleculeName: Transcription activator / type: protein_or_peptide / ID: 1 / Name.synonym: Enhancer-binding protein
Details: Baers following mutations: S160F, R456A, N457A, R461A
Number of copies: 1 / Oligomeric state: Hexamer / Recombinant expression: Yes
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: Bacteria / Cell: Salmonella typhimurium
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.05 mg/mL
BufferpH: 8.2
Details: 200mM KCl, 20mM Tris, 1mM nucleotide, 0.2 mM BeCl2 and 5mM NaF, 5mM MgCl2, 5% Trehalose
StainingType: NEGATIVE / Details: 3% uranyl acetate
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI TECNAI 12
Alignment procedureLegacy - Astigmatism: corrected / Legacy - Electron beam tilt params: 0
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.7 µm / Number real images: 18 / Average electron dose: 20 e/Å2 / Bits/pixel: 14
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 49767 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder: simple tilt / Specimen holder model: OTHER / Tilt angle max: 50

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 3500

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