[English] 日本語
Yorodumi
- EMDB-1109: Structural insights into the activity of enhancer-binding proteins. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1109
TitleStructural insights into the activity of enhancer-binding proteins.
Map datathis is a volume map of PspF in complex with sigma54
Sample
  • Sample: PspF AAA domain
  • Protein or peptide: PspF AAA domain
  • Protein or peptide: sigma54
Function / homologyRNA polymerase sigma factor 54 / AAA+ ATPase domain
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å
AuthorsRappas M / Schumacher J / Beuron F / Niwa H / Bordes P / Wigneshweraraj S / Keetch CA / Robinson CV / Buck M / Zhang X
CitationJournal: Science / Year: 2005
Title: Structural insights into the activity of enhancer-binding proteins.
Authors: Mathieu Rappas / Jorg Schumacher / Fabienne Beuron / Hajime Niwa / Patricia Bordes / Sivaramesh Wigneshweraraj / Catherine A Keetch / Carol V Robinson / Martin Buck / Xiaodong Zhang /
Abstract: Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic ...Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.
History
DepositionFeb 8, 2005-
Header (metadata) releaseFeb 8, 2005-
Map releaseApr 26, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.26
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.26
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1109.gif

Downloads & links

-
Map

FileDownload / File: emd_1109.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is a volume map of PspF in complex with sigma54
Voxel sizeX=Y=Z: 2 Å
Density
Contour Level1: 0.157 / Movie #1: 0.26
Minimum - Maximum-1.00865 - 3.63096
Average (Standard dev.)0.0112357 (±0.146356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 300 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-80-80-80
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean-1.0093.6310.011

-
Supplemental data

-
Sample components

-
Entire : PspF AAA domain

EntireName: PspF AAA domain
Components
  • Sample: PspF AAA domain
  • Protein or peptide: PspF AAA domain
  • Protein or peptide: sigma54

-
Supramolecule #1000: PspF AAA domain

SupramoleculeName: PspF AAA domain / type: sample / ID: 1000
Oligomeric state: one hexamer of PspF binds to a monomer of sigma54
Number unique components: 2
Molecular weightExperimental: 240 KDa / Theoretical: 240 KDa / Method: mass spec

-
Macromolecule #1: PspF AAA domain

MacromoleculeName: PspF AAA domain / type: protein_or_peptide / ID: 1 / Name.synonym: pspf AAA domain / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E Coli
Molecular weightExperimental: 31 KDa / Theoretical: 31 KDa
Recombinant expressionOrganism: Escherichia coli B834 / Recombinant plasmid: pET28 bplus
SequenceInterPro: AAA+ ATPase domain

-
Macromolecule #2: sigma54

MacromoleculeName: sigma54 / type: protein_or_peptide / ID: 2 / Name.synonym: sigma54 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E Coli
Molecular weightExperimental: 54 KDa / Theoretical: 54 KDa
Recombinant expressionOrganism: B834 / Recombinant plasmid: pET28 bplus
SequenceInterPro: RNA polymerase sigma factor 54

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Details: 10 mM Tris HCl, pH8, 50 mM NaCl, 1 mM DTT, 0.1 mM EDTA, 5% glycerol
StainingType: NEGATIVE
Details: Grids with native sample quench frozen in liquid ethane cooled at -186 C
GridDetails: Holey carbon grids from Agar
VitrificationCryogen name: ETHANE / Chamber temperature: 87.15 K / Timed resolved state: vitrified 30msec after / Method: blot for 2 seconds

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/UT
Electron beamAcceleration voltage: 160 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 1.2 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 103 K
Detailsweak beam illumination
DateApr 4, 2002
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 2 µm / Number real images: 9 / Average electron dose: 20 e/Å2 / Bits/pixel: 14

-
Image processing

CTF correctionDetails: Each particle
Final two d classificationNumber classes: 123
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: IMAGIC-5
Details: Final maps were calculate from 123 class averages from one dataset
Number images used: 3895

-
Atomic model buiding 1

DetailsProtocol: Cross correlation coefficient between projections of fitted model and those from the EM reconstruction. The monomer was manually fitted using the program "O"; the model was p6 symmetrised and individually subunits were readjusted manually using "O"
RefinementProtocol: RIGID BODY FIT

+
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