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- EMDB-9039: Mycobacterium tuberculosis RNAP promoter unwinding intermediate c... -

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Basic information

Entry
Database: EMDB / ID: 9039
TitleMycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter
Map dataprimary map
SampleMycobacterium tuberculosis RNAP promoter unwinding intermediate
  • (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 / 3.92 Å resolution
AuthorsDarst SA / Campbell EA / Boyaci Selcuk H / Chen J
CitationJournal: Nature / Year: 2019
Title: Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.
Authors: Hande Boyaci / James Chen / Rolf Jansen / Seth A Darst / Elizabeth A Campbell
Validation ReportPDB-ID: 6ee8

SummaryFull reportAbout validation report
DateDeposition: Aug 13, 2018 / Header (metadata) release: Feb 28, 2018 / Map release: Nov 21, 2018 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ee8
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9039.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 sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-0.42399123 - 1.2823058
Average (Standard dev.)0.006719568 (0.06508604)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin0.00.00.0
Limit249.0249.0249.0
Spacing250250250
CellA=B=C: 325.0 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-0.4241.2820.007

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Supplemental data

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Sample components

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Entire Mycobacterium tuberculosis RNAP promoter unwinding intermediate

EntireName: Mycobacterium tuberculosis RNAP promoter unwinding intermediate
Number of components: 12

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Component #1: protein, Mycobacterium tuberculosis RNAP promoter unwinding inter...

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

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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)

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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)

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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: 148.202219 kDa
SourceSpecies: Mycobacterium tuberculosis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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)

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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)

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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)

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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)

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Component #9: nucleic-acid, DNA (60-MER)

Nucleic-acidName: DNA (60-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)

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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)

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Component #11: ligand, ZINC ION

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

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Component #12: ligand, MAGNESIUM ION

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

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Experimental details

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Sample preparation

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

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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: 1.4 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 140333
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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