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- PDB-4wqt: Thermus thermophilus RNA polymerase complexed with an RNA cleavag... -

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Basic information

Entry
Database: PDB / ID: 4wqt
TitleThermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a GreA/Gfh1 chimeric protein)
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
KeywordsTRANSFERASE/TRANSCRIPTION / transcription / RNA cleavage / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


RNA polymerase binding / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...RNA polymerase binding / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Transcription elongation factor, GreA/GreB, conserved site / Transcription elongation factor, GreA/GreB, N-terminal / Transcription elongation factor, GreA/GreB, N-terminal domain superfamily / Transcription elongation factor, N-terminal / Prokaryotic transcription elongation factors signature 2. / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / : ...Transcription elongation factor, GreA/GreB, conserved site / Transcription elongation factor, GreA/GreB, N-terminal / Transcription elongation factor, GreA/GreB, N-terminal domain superfamily / Transcription elongation factor, N-terminal / Prokaryotic transcription elongation factors signature 2. / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / : / DNA-directed RNA polymerase subunit beta', hybrid 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 superfamily / 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 / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / Transcription inhibitor protein Gfh1 / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.4 Å
AuthorsMurayama, Y. / Sekine, S. / Yokoyama, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science Japan
CitationJournal: Mol.Cell / Year: 2015
Title: The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions.
Authors: Sekine, S.I. / Murayama, Y. / Svetlov, V. / Nudler, E. / Yokoyama, S.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: DNA-directed RNA polymerase subunit alpha
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit beta
I: DNA-directed RNA polymerase subunit beta'
J: DNA-directed RNA polymerase subunit omega
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
X: RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
Y: RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
Z: RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,186,51424
Polymers1,186,24518
Non-polymers2696
Water0
1
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
X: RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,5058
Polymers395,4156
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: DNA-directed RNA polymerase subunit alpha
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit beta
I: DNA-directed RNA polymerase subunit beta'
J: DNA-directed RNA polymerase subunit omega
Y: RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,5058
Polymers395,4156
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: DNA-directed RNA polymerase subunit alpha
L: DNA-directed RNA polymerase subunit alpha
M: DNA-directed RNA polymerase subunit beta
N: DNA-directed RNA polymerase subunit beta'
O: DNA-directed RNA polymerase subunit omega
Z: RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,5058
Polymers395,4156
Non-polymers902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.568, 263.770, 195.848
Angle α, β, γ (deg.)90.00, 116.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 15 molecules ABFGKLCHMDINEJO

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


Mass: 35056.164 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SHR6, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11533.316 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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Protein , 1 types, 3 molecules XYZ

#5: Protein RNA cleavage stimulating factor (GreA/Gfh1 chimeric protein Gre-C1)


Mass: 17335.502 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJG6*PLUS

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Non-polymers , 2 types, 6 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: PEG 6000, potassium chloride, magnesium chloride, HEPES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 104563 / % possible obs: 97 % / Redundancy: 3.3 % / Rsym value: 0.17 / Net I/σ(I): 7
Reflection shellResolution: 4.4→4.56 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.5 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.3refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
CNS1.3phasing
RefinementResolution: 4.4→45.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6361228.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.313 3149 3 %RANDOM
Rwork0.26 ---
obs0.26 104543 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 138.756 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 205.2 Å2
Baniso -1Baniso -2Baniso -3
1--7.05 Å20 Å215.35 Å2
2--8.13 Å20 Å2
3----1.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.89 Å0.79 Å
Luzzati d res low-5 Å
Luzzati sigma a2.13 Å1.53 Å
Refinement stepCycle: LAST / Resolution: 4.4→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms73363 0 6 0 73369
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it15.151.5
X-RAY DIFFRACTIONc_mcangle_it23.492
X-RAY DIFFRACTIONc_scbond_it19.842
X-RAY DIFFRACTIONc_scangle_it28.972.5
LS refinement shellResolution: 4.4→4.68 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.455 488 3 %
Rwork0.433 15841 -
obs--90.5 %

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