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- PDB-8xa8: Cryo-EM structure of Bacillus RNAP and HelD complex -

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Basic information

Entry
Database: PDB / ID: 8xa8
TitleCryo-EM structure of Bacillus RNAP and HelD complex
Components
  • (DNA-directed RNA polymerase subunit ...) x 6
  • DNA helicase IV
KeywordsTRANSCRIPTION / complex
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : ...recombinational repair / 3'-5' DNA helicase activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain ...: / RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit epsilon / DNA helicase IV / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesBacillus (Bacillus rRNA group 1)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsChen, M. / Jin, Q. / Yuan, S. / Liu, B.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270151 China
National Natural Science Foundation of China (NSFC)32270172 China
CitationJournal: To Be Published
Title: A phage encoded sigA-dependent transcription inhibitor also attacks host HelD-mediated defence system
Authors: Chen, M. / Jin, Q. / Zhang, K. / Wang, Y. / Chen, H. / Yu, Z. / Matthews, S. / Yuan, S. / Liu, B.
History
DepositionDec 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit epsilon
F: DNA-directed RNA polymerase subunit omega
H: DNA helicase IV
C: DNA-directed RNA polymerase subunit beta
I: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,64811
Polymers464,4928
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-directed RNA polymerase subunit ... , 6 types, 7 molecules ABDEFCI

#1: Protein DNA-directed RNA polymerase subunit alpha


Mass: 34842.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: rpoA / Production host: Bacillus subtilis (bacteria) / References: UniProt: P20429
#2: Protein DNA-directed RNA polymerase subunit beta'


Mass: 134444.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: rpoC / Production host: Bacillus subtilis (bacteria) / References: UniProt: P37871
#3: Protein DNA-directed RNA polymerase subunit epsilon


Mass: 8277.386 Da / Num. of mol.: 1 / Mutation: V33I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: rnpZA / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A063XGL2
#4: Protein DNA-directed RNA polymerase subunit omega


Mass: 7766.921 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: rpoZ / Production host: Bacillus subtilis (bacteria) / References: UniProt: O35011
#6: Protein DNA-directed RNA polymerase subunit beta


Mass: 133847.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: rpoB / Production host: Bacillus subtilis (bacteria) / References: UniProt: P37870
#7: Protein DNA-directed RNA polymerase subunit delta


Mass: 20417.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: rpoE / Production host: Bacillus subtilis (bacteria) / References: UniProt: P12464

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Protein , 1 types, 1 molecules H

#5: Protein DNA helicase IV


Mass: 90052.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus (Bacillus rRNA group 1) / Gene: helD / Production host: Bacillus subtilis (bacteria) / References: UniProt: O32215

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Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Bacillus RNAP and HelD complex / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Source (natural)Organism: Bacillus (Bacillus rRNA group 1)
Source (recombinant)Organism: Bacillus subtilis (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78265 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429502
ELECTRON MICROSCOPYf_angle_d0.59339933
ELECTRON MICROSCOPYf_dihedral_angle_d4.3594055
ELECTRON MICROSCOPYf_chiral_restr0.0424546
ELECTRON MICROSCOPYf_plane_restr0.0045195

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