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- PDB-8h02: Crystal structure of Synechococcus elongatus PCC 7942 RNA polymer... -

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Basic information

Entry
Database: PDB / ID: 8h02
TitleCrystal structure of Synechococcus elongatus PCC 7942 RNA polymerase SI3-tail
ComponentsDNA-directed RNA polymerase subunit beta'
KeywordsTRANSCRIPTION / RNA polymerase / SI3
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
DNA-directed RNA polymerase, subunit beta'' / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, funnel domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 Å
AuthorsShen, L.Q. / Zhang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2018YFA0900701 China
Other governmentJCYJ-SHFY-2022-012 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: An SI3-σ arch stabilizes cyanobacteria transcription initiation complex.
Authors: Liqiang Shen / Giorgio Lai / Linlin You / Jing Shi / Xiaoxian Wu / Maria Puiu / Zhanxi Gu / Yu Feng / Yulia Yuzenkova / Yu Zhang /
Abstract: Multisubunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all ...Multisubunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all bacterial RNAPs. Here, we report two cryo-EM structures of cyanobacterial transcription initiation complexes at near-atomic resolutions. The structures show that cyanobacterial RNAP forms an "SI3-σ" arch interaction between domain 2 of σ (σ) and sequence insertion 3 (SI3) in the mobile catalytic domain Trigger Loop (TL). The "SI3-σ" arch facilitates transcription initiation from promoters of different classes through sealing the main cleft and thereby stabilizing the RNAP-promoter DNA open complex. Disruption of the "SI3-σ" arch disturbs cyanobacteria growth and stress response. Our study reports the structure of cyanobacterial RNAP and a unique mechanism for its transcription initiation. Our data suggest functional plasticity of SI3 and provide the foundation for further research into cyanobacterial and chloroplast transcription.
History
DepositionSep 27, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit beta'


Theoretical massNumber of molelcules
Total (without water)9,0461
Polymers9,0461
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.133, 32.133, 82.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 9046.376 Da / Num. of mol.: 1 / Fragment: SI3-tail
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: rpoC2, Synpcc7942_1524 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31N15, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium acetate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 11917 / % possible obs: 98.5 % / Redundancy: 7.2 % / CC1/2: 0.981 / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.3
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.165 / Num. unique obs: 609

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AUK

2auk


Resolution: 1.552→32.133 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1194 10.02 %
Rwork0.1976 10723 -
obs0.2 11917 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.01 Å2 / Biso mean: 37.3338 Å2 / Biso min: 19.05 Å2
Refinement stepCycle: final / Resolution: 1.552→32.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms597 0 0 72 669
Biso mean---47.88 -
Num. residues----79
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.552-1.61390.25251360.2093122399
1.6139-1.68730.26681300.20061201100
1.6873-1.77630.24951330.20691194100
1.7763-1.88760.28281370.20191226100
1.8876-2.03330.24581280.20481189100
2.0333-2.23780.24891360.20941198100
2.2378-2.56160.25231310.20111209100
2.5616-3.22680.21981320.2151120097
3.2268-32.1330.19041310.1785108390
Refinement TLS params.Method: refined / Origin x: 12.3059 Å / Origin y: 5.1679 Å / Origin z: 2.4993 Å
111213212223313233
T0.1915 Å20.0113 Å2-0.0086 Å2-0.2201 Å2-0.0147 Å2--0.2343 Å2
L2.7032 °21.026 °21.7366 °2-2.2032 °20.8007 °2--4.0449 °2
S0.0446 Å °0.096 Å °0.0141 Å °0.0575 Å °-0.0402 Å °-0.2291 Å °0.0663 Å °0.2457 Å °0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA352 - 430
2X-RAY DIFFRACTION1allS1 - 81

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