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- EMDB-3561: map of the RNA polymerase lambda-based antitermination complex so... -

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Basic information

Entry
Database: EMDB / ID: 3561
Titlemap of the RNA polymerase lambda-based antitermination complex solved by cryo-EM
SamplelambdaN-dependent antitermination complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map data
Methodsingle particle reconstruction, at 9.8 A resolution
AuthorsSaid N / Krupp F
CitationNat Microbiol, 2017, 2, 17062-17062

Nat Microbiol, 2017, 2, 17062-17062 StrPapers
Structural basis for λN-dependent processive transcription antitermination.
Nelly Said / Ferdinand Krupp / Ekaterina Anedchenko / Karine F Santos / Olexandr Dybkov / Yong-Heng Huang / Chung-Tien Lee / Bernhard Loll / Elmar Behrmann / Jörg Bürger / Thorsten Mielke / Justus Loerke / Henning Urlaub / Christian M T Spahn / Gert Weber / Markus C Wahl

DateDeposition: Dec 29, 2016 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Dec 29, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5ms0
  • Surface level: 0.007
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
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Slabnear <=> far

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Orientation
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Misc. /
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Supplemental images

Downloads & links

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Map

Fileemd_3561.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.28 A/pix
= 307.2 A
240 pix
1.28 A/pix
= 307.2 A
240 pix
1.28 A/pix
= 307.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.28 A
Density
Contour Level:0.007 (by emdb), 0.007 (movie #1):
Minimum - Maximum-0.012556402 - 0.028230608
Average (Standard dev.)0.0003642441 (0.0021255864)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-120-120-120
Limit119119119
Spacing240240240
CellA=B=C: 1 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.281.281.28
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z307.200307.200307.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-0.0130.0280.000

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Supplemental data

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Sample components

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Entire lambdaN-dependent antitermination complex

EntireName: lambdaN-dependent antitermination complex / Number of components: 16

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Component #1: protein, lambdaN-dependent antitermination complex

ProteinName: lambdaN-dependent antitermination complex / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Antitermination protein

ProteinName: Antitermination protein / Details: lambda N factor / Recombinant expression: No
MassTheoretical: 9.877343 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: nucleic-acid, nascent RNA

Nucleic-acidName: nascent RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCUUUAAAA AUAAGCCCUG AAGAAGGGC
MassTheoretical: 9.33965 kDa

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

ProteinName: DNA-directed RNA polymerase subunit alpha / Recombinant expression: No
MassTheoretical: 36.55868 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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

ProteinName: DNA-directed RNA polymerase subunit beta / Recombinant expression: No
MassTheoretical: 150.804922 kDa
Source (engineered)Expression System: Escherichia coli / bacteria /

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Component #6: protein, DNA-directed RNA polymerase subunit beta'

ProteinName: DNA-directed RNA polymerase subunit beta' / Recombinant expression: No
MassTheoretical: 156.537031 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #7: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Recombinant expression: No
MassTheoretical: 11.340067 kDa
Source (engineered)Expression System: Escherichia coli / bacteria /

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Component #8: protein, Transcription termination/antitermination protein NusG

ProteinName: Transcription termination/antitermination protein NusG
Recombinant expression: No
MassTheoretical: 20.688654 kDa
Source (engineered)Expression System: Escherichia coli / bacteria /

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Component #9: nucleic-acid, RNA transcription bubble

Nucleic-acidName: RNA transcription bubble / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAUAAAGACC AGGC
MassTheoretical: 4.492788 kDa

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Component #10: nucleic-acid, DNAI

Nucleic-acidName: DNAI / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DA) (DG)(DT)(DA)(DA)(DA)(DG)(DT)(DA)(DC)(DT) (DT)(DG)(DA)(DG)(DC)(DT)(DT)
MassTheoretical: 8.355408 kDa

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Component #11: nucleic-acid, DNAII

Nucleic-acidName: DNAII / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DG)(DC)(DT)(DC)(DA)(DA)(DG)(DT) (DA)(DC)(DT)(DT)(DA)(DA)(DG)(DC)(DC)(DT) (DG)(DG)(DT)(DC)(DA)(DT)(DT)(DA)(DC)(DT) (DA)(DG)(DT)(DA)(DC)(DT)(DG)(DC)(DC)
MassTheoretical: 11.942696 kDa

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Component #12: protein, N utilization substance protein B homolog

ProteinName: N utilization substance protein B homolog / Recombinant expression: No
MassTheoretical: 15.709967 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #13: protein, Transcription termination/antitermination protein NusA

ProteinName: Transcription termination/antitermination protein NusA
Recombinant expression: No
MassTheoretical: 55.059828 kDa
Source (engineered)Expression System: Escherichia coli / bacteria /

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Component #14: 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 / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #15: ligand, MAGNESIUM ION

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

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Component #16: 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/A2 / 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: 23983
3D reconstructionResolution: 9.8 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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