[English] 日本語
Yorodumi
- EMDB-1218: The structural basis for regulated assembly and function of the t... -

+
Open data


ID or keywords:

Loading...

-
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

-
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

Downloads & links

-
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
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

-
Supplemental data

-
Sample components

-
Entire : Full length, active NtrC

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

-
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

-
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)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more