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- PDB-6ivu: Solution structure of the Sigma-anti-sigma factor complex RsgI1N-... -

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Basic information

Entry
Database: PDB / ID: 6ivu
TitleSolution structure of the Sigma-anti-sigma factor complex RsgI1N-SigI1C from Clostridium thermocellum
Components
  • Anti-sigma-I factor RsgI1
  • RNA polymerase sigma factor SigI1
KeywordsTRANSCRIPTION / sigma factor
Function / homology
Function and homology information


cellulose binding / sigma factor activity / DNA-templated transcription initiation / carbohydrate metabolic process / DNA binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
RNA polymerase sigma-I type / : / Anti-sigma factor RsgI-like central domain / Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. ...RNA polymerase sigma-I type / : / Anti-sigma factor RsgI-like central domain / Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / RNA polymerase sigma factor, region 2
Similarity search - Domain/homology
RNA polymerase sigma factor SigI1 / Anti-sigma-I factor RsgI1
Similarity search - Component
Biological speciesHungateiclostridium thermocellum ATCC 27405 (bacteria)
Clostridium thermocellum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWei, Z. / Feng, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670735 China
National Natural Science Foundation of China31661143023 China
National Natural Science Foundation of China31570029 China
National Natural Science Foundation of China31470210 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Alternative sigma I/anti-sigma I factors represent a unique form of bacterial sigma /anti-sigma complex.
Authors: Wei, Z. / Chen, C. / Liu, Y.J. / Dong, S. / Li, J. / Qi, K. / Liu, S. / Ding, X. / Ortiz de Ora, L. / Munoz-Gutierrez, I. / Li, Y. / Yao, H. / Lamed, R. / Bayer, E.A. / Cui, Q. / Feng, Y.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_spectrometer
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-sigma-I factor RsgI1
B: RNA polymerase sigma factor SigI1


Theoretical massNumber of molelcules
Total (without water)20,3972
Polymers20,3972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1990 Å2
ΔGint-14 kcal/mol
Surface area9780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Anti-sigma-I factor RsgI1


Mass: 6170.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / Gene: Cthe_0059 / Cell line (production host): Rosseta (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A3DBH1
#2: Protein RNA polymerase sigma factor SigI1


Mass: 14226.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: sigI1, Cthe_0058 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A3DBH0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D HN(CA)CO
191isotropic13D HBHA(CO)NH
1101isotropic13D HBHANH
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-COSY
1131isotropic13D CCH-TOCSY
1141isotropic13D CCH-COSY
1151isotropic23D 1H-15N NOESY
1161isotropic23D 1H-13C NOESY aliphatic
1171isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] RsgI1N, 1 mM [U-13C; U-15N] SigI1C, 20 mM Bis-Tris, 50 mM sodium chloride, 2 mM EDTA, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRsgI1N[U-13C; U-15N]1
1 mMSigI1C[U-13C; U-15N]1
20 mMBis-Trisnatural abundance1
50 mMsodium chloridenatural abundance1
2 mMEDTAnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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