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- EMDB-8732: Escherichia coli 6S RNA derivative in complex with Escherichia co... -

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Basic information

Entry
Database: EMDB / ID: 8732
TitleEscherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme
SampleEscherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataprimary map
Methodsingle particle reconstruction, at 3.78 Å resolution
AuthorsChen J / Darst SA
CitationMol. Cell, 2017, 68, 388-397.e6

Mol. Cell, 2017, 68, 388-397.e6 Yorodumi Papers
6S RNA Mimics B-Form DNA to Regulate Escherichia coli RNA Polymerase.
James Chen / Karen M Wassarman / Shili Feng / Katherine Leon / Andrey Feklistov / Jared T Winkelman / Zongli Li / Thomas Walz / Elizabeth A Campbell / Seth A Darst

Validation ReportPDB-ID: 5vt0

SummaryFull reportAbout validation report
DateDeposition: May 15, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Nov 1, 2017 / Last update: Nov 1, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5vt0
  • Surface level: 0.017
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8732.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.014 (by author), 0.017 (movie #1):
Minimum - Maximum-0.07076079 - 0.11960874
Average (Standard dev.)0.00019718395 (0.0041868477)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0710.1200.000

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Supplemental data

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Sample components

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Entire Escherichia coli 6S RNA derivative in complex with Escherichia co...

EntireName: Escherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme
Number of components: 9
MassExperimental: 475 kDa

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Component #1: protein, Escherichia coli 6S RNA derivative in complex with Esche...

ProteinName: Escherichia coli 6S RNA derivative in complex with Escherichia coli RNA polymerase sigma70-holoenzyme
Recombinant expression: No
MassExperimental: 475 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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

ProteinName: DNA-directed RNA polymerase subunit alpha / Recombinant expression: No
MassTheoretical: 26.330996 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

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

ProteinName: DNA-directed RNA polymerase subunit beta / Recombinant expression: No
MassTheoretical: 150.820875 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

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

ProteinName: DNA-directed RNA polymerase subunit beta' / Recombinant expression: No
MassTheoretical: 155.366781 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

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

ProteinName: DNA-directed RNA polymerase subunit omega / Recombinant expression: No
MassTheoretical: 10.249547 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

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Component #6: protein, RNA polymerase sigma factor RpoD

ProteinName: RNA polymerase sigma factor RpoD / Recombinant expression: No
MassTheoretical: 60.464371 kDa
Source (engineered)Expression System: Escherichia coli (strain k12) / bacteria /
Strain: K12

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Component #7: nucleic-acid, Escherichia coli 6S RNA derivative (112-MER)

Nucleic-acidName: Escherichia coli 6S RNA derivative (112-MER) / Class: RNA / Details: prepared by in vitro transcription / Structure: OTHER / Synthetic: No
Sequence:
GGACUCCCAG UCGGCACAUG CGAUAUUUCA UACCACAAGA AUGUGGCGCU CCGCGGUUGG UGAGCAUGCU CGGUCCGUCC GAGAAGCCUU AAAACUGCGA CGACACAUUC ACCUUGAACC AAGGCGUGUA CCGUUACAGG GGUC
MassTheoretical: 46.3085 kDa

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Component #8: ligand, MAGNESIUM ION

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

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Component #9: ligand, ZINC ION

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

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 8
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: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 362926
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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