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- PDB-5ms0: pseudo-atomic model of the RNA polymerase lambda-based antitermin... -

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Basic information

Entry
Database: PDB / ID: 5ms0
Titlepseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM
DescriptorAntitermination protein
30S ribosomal protein S10
N utilization substance protein B homolog
(DNA-directed RNA polymerase subunit ...) x 4
(Transcription termination/antitermination protein ...) x 2
KeywordsTRANSCRIPTION/DNA/RNA / DNA-DEPENDENT RNA POLYMERASE / BACTERIAL TRANSCRIPTION / TERNARY ELONGATION COMPLEX / ANTITERMINATION / TRANSCRIPTION-DNA-RNA complex
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (9.8 Å resolution / Particle / Single particle)
AuthorsSaid, N. / Krupp, F.
CitationNat Microbiol, 2017, 2, 17062-17062

Nat Microbiol, 2017, 2, 17062-17062 Yorodumi Papers
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 29, 2016 / Release: May 3, 2017
RevisionDateData content typeGroupProviderType
1.0May 3, 2017Structure modelrepositoryInitial release
1.1May 10, 2017Structure modelDatabase references

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Assembly

Deposited unit
N: Antitermination protein
R: nascent RNA
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: 30S ribosomal protein S10
F: Transcription termination/antitermination protein NusG
H: RNA transcription bubble
I: DNAI
J: DNAII
L: N utilization substance protein B homolog
M: Transcription termination/antitermination protein NusA
O: DNA-directed RNA polymerase subunit omega
hetero molecules


Theoretical massNumber of molelcules
Total (without water)537,67017
Polyers537,51514
Non-polymers1553
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polypeptide(L) , 3 types, 3 molecules NEL

#1: Polypeptide(L)Antitermination protein


Mass: 9877.343 Da / Num. of mol.: 1 / Details: lambda N factor / Source: (gene. exp.) Escherichia coli / References: UniProt: A0A0L6XR33

Molecular function

Biological process

#6: Polypeptide(L)30S ribosomal protein S10 / Small ribosomal subunit protein uS10


Mass: 11340.067 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0A7R5

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)N utilization substance protein B homolog / Protein NusB


Mass: 15709.967 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: B7MD74

Cellular component

Molecular function

Biological process

  • DNA-templated transcription, termination (GO: 0006353)
  • regulation of transcription, DNA-templated (GO: 0006355)

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RNA chain , 2 types, 2 molecules RH

#2: RNA chainnascent RNA


Mass: 9339.650 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli
#8: RNA chainRNA transcription bubble


Mass: 4492.788 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDO

#3: Polypeptide(L)DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0A7Z4, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150804.922 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0A8V2, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 156537.031 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0A8T8, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0A800, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

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Transcription termination/antitermination protein ... , 2 types, 2 molecules FM

#7: Polypeptide(L)Transcription termination/antitermination protein NusG


Mass: 20688.654 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AFG0

Cellular component

Biological process

#12: Polypeptide(L)Transcription termination/antitermination protein NusA / N utilization substance protein A / Transcription termination/antitermination L factor


Mass: 55059.828 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: P0AFF6

Cellular component

Molecular function

Biological process

  • transcription antitermination (GO: 0031564)
  • transcription termination from bacterial-type RNA polymerase promoter (GO: 0001125)

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DNA chain , 2 types, 2 molecules IJ

#9: DNA chainDNAI


Mass: 8355.408 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli
#10: DNA chainDNAII


Mass: 11942.696 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli

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Non-polymers , 2 types, 3 molecules

#14: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg
#15: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: lambdaN-dependent antitermination complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.5
SpecimenDetails: 10 mM HEPES-NaOH, pH 7.5, 50 mM NaCl, 1 mM DTT / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 23983 / Symmetry type: POINT

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