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- PDB-4wqs: Thermus thermophilus RNA polymerase backtracked complex -

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Basic information

Entry
Database: PDB / ID: 4wqs
TitleThermus thermophilus RNA polymerase backtracked complex
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • DNA (28-MER)
  • DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')
  • RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')
KeywordsTRANSFERASE/DNA/RNA / transcription / RNA cleavage / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / 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 / cytoplasm
Similarity search - Function
: / 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 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 / DNA (> 10) / RNA / RNA (> 10) / DNA-directed RNA polymerase subunit alpha / 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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.306 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 1.1Sep 9, 2015Group: Derived calculations
Revision 1.2Sep 16, 2015Group: Other
Revision 1.3Dec 4, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / ndb_struct_na_base_pair ...diffrn_source / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site / _ndb_struct_na_base_pair.hbond_type_12 ..._diffrn_source.pdbx_synchrotron_site / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.tip / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 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
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
G: DNA (28-MER)
H: RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')
I: DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')
X: DNA (28-MER)
Y: RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')
Z: DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)796,83420
Polymers796,57316
Non-polymers2624
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
G: DNA (28-MER)
H: RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')
I: DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,41710
Polymers398,2868
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42170 Å2
ΔGint-225 kcal/mol
Surface area130450 Å2
MethodPISA
2
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: DNA (28-MER)
Y: RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')
Z: DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,41710
Polymers398,2868
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39480 Å2
ΔGint-170 kcal/mol
Surface area142340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.983, 155.983, 495.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABKLCMDNEO

#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.: 4 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / References: UniProt: Q8RQE7, DNA-directed RNA polymerase

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DNA chain , 2 types, 4 molecules GXIZ

#5: DNA chain DNA (28-MER)


Mass: 8545.510 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#7: DNA chain DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')


Mass: 6574.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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RNA chain / Non-polymers , 2 types, 6 molecules HY

#6: RNA chain RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')


Mass: 5087.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG-8000, calcium chloride, 1,6-hexanediol, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / % possible obs: 99.7 % / Redundancy: 9.1 % / Rsym value: 0.175 / Net I/σ(I): 11.9
Reflection shellResolution: 4.3→4.45 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
CNS1.3phasing
RefinementResolution: 4.306→44.15 Å / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 31.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3114 3821 4.82 %
Rwork0.2805 --
obs0.2825 79319 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.306→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45694 2468 4 0 48166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149266
X-RAY DIFFRACTIONf_angle_d1.74167149
X-RAY DIFFRACTIONf_dihedral_angle_d20.41319210
X-RAY DIFFRACTIONf_chiral_restr0.1187594
X-RAY DIFFRACTIONf_plane_restr0.0118381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3065-4.38070.30991670.33483755X-RAY DIFFRACTION96
4.3807-4.46020.34771870.32383831X-RAY DIFFRACTION95
4.4602-4.54590.33751880.31773727X-RAY DIFFRACTION95
4.5459-4.63860.31041760.30933761X-RAY DIFFRACTION96
4.6386-4.73930.31672070.30483784X-RAY DIFFRACTION95
4.7393-4.84940.29532030.30243749X-RAY DIFFRACTION95
4.8494-4.97050.31461980.29733767X-RAY DIFFRACTION95
4.9705-5.10470.28871660.29783790X-RAY DIFFRACTION96
5.1047-5.25460.34372330.30023742X-RAY DIFFRACTION94
5.2546-5.42390.30591680.28873785X-RAY DIFFRACTION96
5.4239-5.61730.31161740.29983794X-RAY DIFFRACTION96
5.6173-5.84170.32942190.29063739X-RAY DIFFRACTION94
5.8417-6.10680.32191720.30313801X-RAY DIFFRACTION96
6.1068-6.42780.33022350.29863720X-RAY DIFFRACTION94
6.4278-6.82890.33891880.30223791X-RAY DIFFRACTION95
6.8289-7.35370.34271840.29723777X-RAY DIFFRACTION95
7.3537-8.0890.35581850.28913800X-RAY DIFFRACTION95
8.089-9.24890.2781860.27323785X-RAY DIFFRACTION95
9.2489-11.61270.27561900.23373794X-RAY DIFFRACTION95
11.6127-42.33820.29631950.23723793X-RAY DIFFRACTION95

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