[English] 日本語
Yorodumi
- PDB-6ccv: Crystal structure of a Mycobacterium smegmatis RNA polymerase tra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ccv
TitleCrystal structure of a Mycobacterium smegmatis RNA polymerase transcription initiation complex with inhibitor Rifampicin
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • DNA (26-MER)
  • DNA (31-MER)
  • RNA polymerase sigma factor SigA
  • RNA polymerase-binding protein RbpA
  • Unknown Peptide
KeywordsTRANSCRIPTION / DNA-directed RNA polymerase tuberculosis inhibitor antibiotic transcription initiation
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / sigma factor activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription initiation / DNA-templated transcription / protein dimerization activity / response to antibiotic / positive regulation of DNA-templated transcription ...bacterial-type RNA polymerase core enzyme binding / sigma factor activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription initiation / DNA-templated transcription / protein dimerization activity / response to antibiotic / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase-binding protein / RNA polymerase-binding protein RbpA / RbpA superfamily / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit ...RNA polymerase-binding protein / RNA polymerase-binding protein RbpA / RbpA superfamily / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Sigma-70 factors family signature 2. / Sigma-70 region 3 / RNA polymerase sigma-70 region 3 / RNA polymerase sigma-70 / Sigma-70, region 4 / RNA polymerase sigma-70 region 4 / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Sigma-70 region 2 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase, alpha subunit, C-terminal / Gyrase A; domain 2 / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 3 superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase, alpha subunit / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / RNA polymerases D / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / Beta Complex / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit alpha / GLUTAMIC ACID / DNA-directed RNA polymerase subunit beta' / DNA (> 10) / DNA / RIFAMPICIN / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Mycobacterium smegmatis str. MC2 155 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLilic, M. / Darst, S.A. / Campbell, E.A.
CitationJournal: Nat Commun / Year: 2018
Title: Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
Authors: Peek, J. / Lilic, M. / Montiel, D. / Milshteyn, A. / Woodworth, I. / Biggins, J.B. / Ternei, M.A. / Calle, P.Y. / Danziger, M. / Warrier, T. / Saito, K. / Braffman, N. / Fay, A. / Glickman, ...Authors: Peek, J. / Lilic, M. / Montiel, D. / Milshteyn, A. / Woodworth, I. / Biggins, J.B. / Ternei, M.A. / Calle, P.Y. / Danziger, M. / Warrier, T. / Saito, K. / Braffman, N. / Fay, A. / Glickman, M.S. / Darst, S.A. / Campbell, E.A. / Brady, S.F.
History
DepositionFeb 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2May 15, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor SigA
G: Unknown Peptide
J: RNA polymerase-binding protein RbpA
O: DNA (31-MER)
P: DNA (26-MER)
T: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,27536
Polymers484,42911
Non-polymers2,84625
Water25214
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)132.353, 162.325, 139.401
Angle α, β, γ (deg.)90.00, 107.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
DNA-directed RNA polymerase subunit ... , 4 types, 6 molecules ABTCDE

#1: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 37959.441 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QSL8, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 128680.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: P60281, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 146712.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QS66, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11544.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QWT1, DNA-directed RNA polymerase

-
Protein , 2 types, 2 molecules FJ

#5: Protein RNA polymerase sigma factor SigA


Mass: 51573.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: sigA, MSMEG_2758 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QW02
#7: Protein RNA polymerase-binding protein RbpA


Mass: 13078.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: rbpA, MSMEG_3858, MSMEI_3768 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QZ11

-
Protein/peptide , 1 types, 1 molecules G

#6: Protein/peptide Unknown Peptide


Mass: 1464.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Production host: Escherichia coli (E. coli)

-
DNA chain , 2 types, 2 molecules OP

#8: DNA chain DNA (31-MER)


Mass: 9565.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA (26-MER)


Mass: 7930.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 39 molecules

#10: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#11: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#12: Chemical ChemComp-RFP / RIFAMPICIN / Rifampicin


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#13: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#14: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris, pH 6.0, 0.2 M LiSO4, 16% (w/v) polyetheylene glycol 3350, 2.5% (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97992 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97992 Å / Relative weight: 1
ReflectionResolution: 3.05→55 Å / Num. obs: 106159 / % possible obs: 97.95 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1518 / Rpim(I) all: 0.05852 / Net I/σ(I): 13.86
Reflection shellResolution: 3.05→3.16 Å / Rmerge(I) obs: 2.285 / Num. unique obs: 55184 / CC1/2: 0.503 / Rpim(I) all: 1.026

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TW1
Resolution: 3.05→57.119 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1741 1.66 %
Rwork0.2231 --
obs0.2239 104824 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→57.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25193 1160 167 14 26534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227042
X-RAY DIFFRACTIONf_angle_d0.50736929
X-RAY DIFFRACTIONf_dihedral_angle_d13.9416220
X-RAY DIFFRACTIONf_chiral_restr0.0384271
X-RAY DIFFRACTIONf_plane_restr0.0034641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.13970.38641180.36267070X-RAY DIFFRACTION81
3.1397-3.24110.3311490.30728524X-RAY DIFFRACTION97
3.2411-3.35690.36471360.29098712X-RAY DIFFRACTION100
3.3569-3.49130.30951500.2668751X-RAY DIFFRACTION100
3.4913-3.65020.26911520.26238708X-RAY DIFFRACTION100
3.6502-3.84260.32331440.25578746X-RAY DIFFRACTION100
3.8426-4.08330.291500.2398679X-RAY DIFFRACTION99
4.0833-4.39840.27941490.21348745X-RAY DIFFRACTION100
4.3984-4.84080.2561430.20298723X-RAY DIFFRACTION100
4.8408-5.54080.25381460.21828762X-RAY DIFFRACTION99
5.5408-6.97890.28561540.2238809X-RAY DIFFRACTION100
6.9789-57.12940.20631500.17148854X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more