[English] 日本語
Yorodumi
- PDB-3t72: PhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t72
TitlePhoB(E)-Sigma70(4)-(RNAP-Betha-flap-tip-helix)-DNA Transcription Activation Sub-Complex
Components
  • PHO BOX DNA (STRAND 1)
  • PHO BOX DNA (STRAND 2)
  • Phosphate regulon transcriptional regulatory protein phoB
  • RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta
KeywordsTRANSCRIPTION/DNA / WINGED-HELIX MOTIF / TRANSCRIPTION ACTIVATION / DNA-BINDING / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / sigma factor antagonist complex / phosphorelay response regulator activity / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-templated transcription initiation / protein-DNA complex / response to heat ...bacterial-type RNA polymerase holo enzyme binding / phosphate ion transport / sigma factor antagonist complex / phosphorelay response regulator activity / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-templated transcription initiation / protein-DNA complex / response to heat / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding / cytosol
Similarity search - Function
Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 ...Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Transcriptional regulatory protein WalR-like / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / : / RNA polymerase sigma factor RpoD / Phosphate regulon transcriptional regulatory protein PhoB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 4.33 Å
AuthorsBlanco, A.G. / Canals, A. / Bernues, J. / Sola, M. / Coll, M.
CitationJournal: Embo J. / Year: 2011
Title: The structure of a transcription activation subcomplex reveals how sigma (70) is recruited to PhoB promoters.
Authors: Blanco, A.G. / Canals, A. / Bernues, J. / Sola, M. / Coll, M.
History
DepositionJul 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Derived calculations
Revision 1.2Dec 18, 2013Group: Structure summary
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jul 26, 2023Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphate regulon transcriptional regulatory protein phoB
B: Phosphate regulon transcriptional regulatory protein phoB
C: PHO BOX DNA (STRAND 1)
D: PHO BOX DNA (STRAND 2)
E: Phosphate regulon transcriptional regulatory protein phoB
F: Phosphate regulon transcriptional regulatory protein phoB
G: PHO BOX DNA (STRAND 1)
H: PHO BOX DNA (STRAND 2)
I: Phosphate regulon transcriptional regulatory protein phoB
J: Phosphate regulon transcriptional regulatory protein phoB
K: PHO BOX DNA (STRAND 1)
L: PHO BOX DNA (STRAND 2)
M: Phosphate regulon transcriptional regulatory protein phoB
N: Phosphate regulon transcriptional regulatory protein phoB
O: PHO BOX DNA (STRAND 1)
P: PHO BOX DNA (STRAND 2)
R: Phosphate regulon transcriptional regulatory protein phoB
S: Phosphate regulon transcriptional regulatory protein phoB
T: PHO BOX DNA (STRAND 1)
U: PHO BOX DNA (STRAND 2)
V: Phosphate regulon transcriptional regulatory protein phoB
W: Phosphate regulon transcriptional regulatory protein phoB
X: PHO BOX DNA (STRAND 1)
Y: PHO BOX DNA (STRAND 2)
Z: Phosphate regulon transcriptional regulatory protein phoB
1: Phosphate regulon transcriptional regulatory protein phoB
2: PHO BOX DNA (STRAND 1)
3: PHO BOX DNA (STRAND 2)
4: Phosphate regulon transcriptional regulatory protein phoB
5: Phosphate regulon transcriptional regulatory protein phoB
6: PHO BOX DNA (STRAND 1)
7: PHO BOX DNA (STRAND 2)
8: Phosphate regulon transcriptional regulatory protein phoB
9: Phosphate regulon transcriptional regulatory protein phoB
a: PHO BOX DNA (STRAND 1)
b: PHO BOX DNA (STRAND 2)
c: Phosphate regulon transcriptional regulatory protein phoB
d: Phosphate regulon transcriptional regulatory protein phoB
e: PHO BOX DNA (STRAND 1)
f: PHO BOX DNA (STRAND 2)
g: Phosphate regulon transcriptional regulatory protein phoB
h: Phosphate regulon transcriptional regulatory protein phoB
i: PHO BOX DNA (STRAND 1)
j: PHO BOX DNA (STRAND 2)
k: Phosphate regulon transcriptional regulatory protein phoB
l: Phosphate regulon transcriptional regulatory protein phoB
m: PHO BOX DNA (STRAND 1)
n: PHO BOX DNA (STRAND 2)
o: RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta
q: RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta


Theoretical massNumber of molelcules
Total (without water)501,14850
Polymers501,14850
Non-polymers00
Water00
1
A: Phosphate regulon transcriptional regulatory protein phoB
B: Phosphate regulon transcriptional regulatory protein phoB
C: PHO BOX DNA (STRAND 1)
D: PHO BOX DNA (STRAND 2)
q: RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta


Theoretical massNumber of molelcules
Total (without water)50,9965
Polymers50,9965
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Phosphate regulon transcriptional regulatory protein phoB
F: Phosphate regulon transcriptional regulatory protein phoB
G: PHO BOX DNA (STRAND 1)
H: PHO BOX DNA (STRAND 2)
o: RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta


Theoretical massNumber of molelcules
Total (without water)50,9965
Polymers50,9965
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Phosphate regulon transcriptional regulatory protein phoB
J: Phosphate regulon transcriptional regulatory protein phoB
K: PHO BOX DNA (STRAND 1)
L: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Phosphate regulon transcriptional regulatory protein phoB
N: Phosphate regulon transcriptional regulatory protein phoB
O: PHO BOX DNA (STRAND 1)
P: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
R: Phosphate regulon transcriptional regulatory protein phoB
S: Phosphate regulon transcriptional regulatory protein phoB
T: PHO BOX DNA (STRAND 1)
U: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
V: Phosphate regulon transcriptional regulatory protein phoB
W: Phosphate regulon transcriptional regulatory protein phoB
X: PHO BOX DNA (STRAND 1)
Y: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Z: Phosphate regulon transcriptional regulatory protein phoB
1: Phosphate regulon transcriptional regulatory protein phoB
2: PHO BOX DNA (STRAND 1)
3: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
4: Phosphate regulon transcriptional regulatory protein phoB
5: Phosphate regulon transcriptional regulatory protein phoB
6: PHO BOX DNA (STRAND 1)
7: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
8: Phosphate regulon transcriptional regulatory protein phoB
9: Phosphate regulon transcriptional regulatory protein phoB
a: PHO BOX DNA (STRAND 1)
b: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
c: Phosphate regulon transcriptional regulatory protein phoB
d: Phosphate regulon transcriptional regulatory protein phoB
e: PHO BOX DNA (STRAND 1)
f: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
g: Phosphate regulon transcriptional regulatory protein phoB
h: Phosphate regulon transcriptional regulatory protein phoB
i: PHO BOX DNA (STRAND 1)
j: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
k: Phosphate regulon transcriptional regulatory protein phoB
l: Phosphate regulon transcriptional regulatory protein phoB
m: PHO BOX DNA (STRAND 1)
n: PHO BOX DNA (STRAND 2)


Theoretical massNumber of molelcules
Total (without water)39,9164
Polymers39,9164
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)277.300, 161.400, 260.100
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is that formed by chains A,B,C,D,q and r

-
Components

#1: Protein ...
Phosphate regulon transcriptional regulatory protein phoB / Coordinate model: Cα atoms only


Mass: 11971.624 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: phoB, b0399, JW0389 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFJ5
#2: DNA chain
PHO BOX DNA (STRAND 1)


Mass: 8035.216 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Synthesized DNA / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain
PHO BOX DNA (STRAND 2)


Mass: 7937.140 Da / Num. of mol.: 12 / Source method: obtained synthetically / Details: Synthesized DNA / Source: (synth.) Escherichia coli (E. coli)
#4: Protein RNA polymerase sigma factor rpoD, DNA-directed RNA polymerase subunit beta / Sigma-70 / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta / Coordinate model: Cα atoms only


Mass: 11080.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpoD, alt, b3067, JW3039, EKO11_4334, rpoB / Production host: Escherichia coli (E. coli)
References: UniProt: P00579, UniProt: E8Y6A0, DNA-directed RNA polymerase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.81 Å3/Da / Density % sol: 78.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 8-10% PEG 4000, 100 mM KCl, 10 mM magnesium chloride, 50 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2542,1.2554,1.2498
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2006
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25421
21.25541
31.24981
ReflectionResolution: 4.33→50 Å / Num. all: 73615 / Num. obs: 73615 / % possible obs: 100 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5

-
Processing

Software
NameClassification
DNAdata collection
SHELXSphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 4.33→50 Å / Num. reflection obs: 73615
Details: CLOSE CONTACTS OF DNA ATOMS WITH SYMMETRY-EQUIVALENT NEIGHBOUR DNA MOLECULES FORMING PSEUDO-CONTINUOUS HELICES ARE DUE TO LACK OF ATOMIC POSITIONAL REFINEMENT
Refinement stepCycle: LAST / Resolution: 4.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 12720 0 0 15354

+
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