[English] 日本語
Yorodumi
- EMDB-9037: Mycobacterium tuberculosis RNAP open promoter complex with RbpA/C... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 9037
TitleMycobacterium tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter
Map data
SampleMycobacterium tuberculosis RNAP open promoter complex
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • RNA polymerase sigma factor SigA
  • (RNA polymerase-binding ...) x 2
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 2
Function / homologyRNA polymerase Rpb2, OB-fold / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / Winged helix-like DNA-binding domain superfamily / RPB6/omega subunit-like superfamily / CarD-like/TRCF domain superfamily / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb2, domain 2 superfamily ...RNA polymerase Rpb2, OB-fold / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / Winged helix-like DNA-binding domain superfamily / RPB6/omega subunit-like superfamily / CarD-like/TRCF domain superfamily / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2 / RNA polymerase sigma-70 like domain / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / RNA polymerase sigma factor RpoD, C-terminal / DNA-directed RNA polymerase, subunit beta-prime / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 1 / Sigma-70 region 3 / RNA polymerase Rpb2, domain 3 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / Sigma-70, region 4 / Sigma-70 region 2 / Bacterial RNA polymerase, alpha chain C terminal domain / RbpA superfamily / CarD-like/TRCF domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / Sigma-70 factor, region 1.2 / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb1, domain 1 / RNA polymerases beta chain signature. / Sigma-70 factors family signature 2. / Sigma-70 factors family signature 1. / RNA polymerase-binding protein / RNA polymerase beta subunit external 1 domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase, alpha subunit / RNA polymerase sigma-70 / CarD-like/TRCF domain / DNA-directed RNA polymerase, omega subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase, N-terminal / DNA-directed RNA polymerase, insert domain / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, alpha subunit, C-terminal / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase sigma-70 region 1.2 / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / RNA polymerase sigma-70 region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 region 3 / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / bacterial-type RNA polymerase core enzyme binding / transcription initiation from bacterial-type RNA polymerase promoter / sigma factor activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / pathogenesis / protein dimerization activity / transcription, DNA-templated / DNA-binding transcription factor activity / positive regulation of transcription, DNA-templated / DNA binding / cytoplasm / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / RNA polymerase-binding protein RbpA / RNA polymerase-binding transcription factor CarD / DNA-directed RNA polymerase subunit beta
Function and homology information
SourceMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM
AuthorsDarst SA / Campbell EA / Boyaci Selcuk H / Chen J
CitationJournal: To Be Published
Title: The path and dynamics of promoter unwinding captured by structural intermediates
Authors: Darst SA / Campbell E / Boyaci Selcuk H / Chen J
Validation ReportPDB-ID: 6edt

SummaryFull reportAbout validation report
DateDeposition: Aug 10, 2018 / Header (metadata) release: Feb 28, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6edt
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_9037.map.gz (map file in CCP4 format, 62501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.3 Å/pix.
= 325. Å
250 pix
1.3 Å/pix.
= 325. Å
250 pix
1.3 Å/pix.
= 325. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.071.071.07
CCP4 map header1.31.31.3
EM Navigator Movie #11.31.31.3
Density
Contour Level:0.25 (by author), 0.3 (movie #1):
Minimum - Maximum-0.7299977 - 1.9311254
Average (Standard dev.)0.006558573 (0.07501595)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin0.00.00.0
Limit249.0249.0249.0
Spacing250250250
CellA=B=C: 267.5 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z325.000325.000325.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.7301.9310.007

-
Supplemental data

-
Sample components

+
Entire Mycobacterium tuberculosis RNAP open promoter complex

EntireName: Mycobacterium tuberculosis RNAP open promoter complex / Number of components: 12

+
Component #1: protein, Mycobacterium tuberculosis RNAP open promoter complex

ProteinName: Mycobacterium tuberculosis RNAP open promoter complex / Recombinant expression: No
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #2: protein, DNA-directed RNA polymerase subunit alpha

ProteinName: DNA-directed RNA polymerase subunit alphaPolymerase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 37.745328 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 125.390875 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, DNA-directed RNA polymerase subunit beta'

ProteinName: DNA-directed RNA polymerase subunit beta'Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 152.882109 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, DNA-directed RNA polymerase subunit omega

ProteinName: DNA-directed RNA polymerase subunit omegaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.776996 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #6: protein, RNA polymerase sigma factor SigA

ProteinName: RNA polymerase sigma factor SigA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.169477 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #7: protein, RNA polymerase-binding protein RbpA

ProteinName: RNA polymerase-binding protein RbpA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.993695 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #8: nucleic-acid, DNA (65-MER)

Nucleic-acidName: DNA (65-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DC)(DT)(DA)(DT)(DG)(DG)(DA)(DT) (DG)(DA)(DC)(DC)(DG)(DA)(DA)(DC)(DC)(DT) (DG)(DG)(DT)(DC)(DT)(DT)(DG)(DA)(DC)(DT) (DC)(DC)(DA)(DT)(DT)(DG)(DC)(DC)(DG)(DG) (DA)(DT)(DT)(DT)(DG)(DT)(DA)(DT)(DT)(DA) (DG)(DA)(DC)(DT)(DG)(DG)(DC)(DA)(DG)(DG) (DG)(DT)(DT)(DG)(DC)(DC)(DC)(DC)(DG)(DA) (DA)(DG)(DC)(DG)(DG)(DG)(DC)(DG)(DG)(DA) (DA)(DA)(DC)(DA)(DA)(DG)(DC)(DA)(DC)(DG)
MassTheoretical: 27.907809 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)

+
Component #9: nucleic-acid, DNA (65-MER)

Nucleic-acidName: DNA (65-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DG)(DT)(DG)(DC)(DT)(DT)(DG)(DT)(DT) (DT)(DC)(DC)(DG)(DC)(DC)(DC)(DG)(DC)(DT) (DT)(DC)(DG)(DG)(DG)(DG)(DC)(DA)(DA)(DC) (DC)(DC)(DT)(DG)(DC)(DC)(DA)(DG)(DT)(DC) (DT)(DA)(DA)(DT)(DA)(DC)(DA)(DA)(DA)(DT) (DC)(DC)(DG)(DG)(DC)(DA)(DA)(DT)(DG)(DG) (DA)(DG)(DT)(DC)(DA)(DA)(DG)(DA)(DC)(DC) (DA)(DG)(DG)(DT)(DT)(DC)(DG)(DG)(DT)(DC) (DA)(DT)(DC)(DC)(DA)(DT)(DA)(DG)(DC)(DC)
MassTheoretical: 27.618625 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)

+
Component #10: protein, RNA polymerase-binding transcription factor CarD

ProteinName: RNA polymerase-binding transcription factor CarD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.933361 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #11: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #12: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 69.9 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 211381

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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