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- PDB-4xlq: Crystal structure of T.aquaticus transcription initiation complex... -

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Basic information

Entry
Database: PDB / ID: 4xlq
TitleCrystal structure of T.aquaticus transcription initiation complex containing upstream fork (-11 base-paired) promoter
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • DNA (26-MER)
  • DNA (30-MER)
  • RNA polymerase sigma factor SigA
Keywordstranscription/DNA / protein-DNA complex / Bacterial transcription initiation complex / transcription-DNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / 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 / 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 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 ...: / DNA-directed RNA polymerase subunit beta', hybrid domain / 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 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.6 Å
Model details5' end of template strand is at -11
AuthorsBae, B. / Darst, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053759 United States
CitationJournal: Elife / Year: 2015
Title: Structure of a bacterial RNA polymerase holoenzyme open promoter complex.
Authors: Bae, B. / Feklistov, A. / Lass-Napiorkowska, A. / Landick, R. / Darst, S.A.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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: RNA polymerase sigma factor SigA
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor SigA
O: DNA (30-MER)
P: DNA (26-MER)
R: DNA (30-MER)
S: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)869,24522
Polymers868,93516
Non-polymers3106
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
F: RNA polymerase sigma factor SigA
O: DNA (30-MER)
P: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,62311
Polymers434,4688
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52490 Å2
ΔGint-224 kcal/mol
Surface area149450 Å2
MethodPISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor SigA
R: DNA (30-MER)
S: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,62311
Polymers434,4688
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53330 Å2
ΔGint-223 kcal/mol
Surface area142650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)288.230, 288.230, 535.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' or chain 'B' or (chain 'C' and (resseq...
211chain 'G' or chain 'H' or (chain 'I' and (resseq...
112chain 'C' and (resseq 22:130 or resseq 336:392)
212chain 'I' and (resseq 22:130 or resseq 336:392)
113chain 'C' and (resseq 143:324)
213chain 'I' and (resseq 143:324)
114(chain 'C' and resseq 703:830) or (chain 'F' and resseq 335:423)
214(chain 'I' and resseq 703:830) or (chain 'L' and resseq 335:423)
115(chain 'C' and resseq 1058:1119) or (chain 'D' and (resseq...
215(chain 'I' and resseq 1058:1119) or (chain 'J' and (resseq...

NCS ensembles :
ID
1
2
3
4
5
Detailsbiological unit is a hetero 6-mer. There are 2 biological units in the asymmetric unit (chains ABCDEFOP and GHIJKLRS

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Components

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

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


Mass: 34830.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 124930.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11642.423 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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Protein , 1 types, 2 molecules FL

#5: Protein RNA polymerase sigma factor SigA


Mass: 39864.730 Da / Num. of mol.: 2 / Fragment: unp residues 92-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: sigA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EZJ8

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DNA chain , 2 types, 4 molecules ORPS

#6: DNA chain DNA (30-MER) / DNA non-template strand


Mass: 9235.988 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA non-template strand / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (26-MER) / DNA template strand


Mass: 7945.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 6 molecules

#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 6.39 Å3/Da / Density % sol: 80.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: ammonium sulfate, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.5→50 Å / Num. obs: 135196 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 154.57 Å2 / Rmerge(I) obs: 0.224 / Χ2: 1.058 / Net I/av σ(I): 3.3 / Net I/σ(I): 1.8 / Num. measured all: 1367979
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
4.5-4.669.9133310.86799.8
4.66-4.8510.1133140.8799.9
4.85-5.0710.2133470.88299.9
5.07-5.3310.3133700.87699.9
5.33-5.6710.4134310.999.9
5.67-6.1110.3134510.92799.9
6.11-6.7210.3135000.94499.9
6.72-7.6910.2135450.9881000.805
7.69-9.6710137241.3081000.257
9.67-509.5141832.0381000.113

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.6→49.807 Å / SU ML: 0.85 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 6221 5.04 %
Rwork0.2449 --
obs0.2467 123358 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.6→49.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54208 2263 6 0 56477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00557731
X-RAY DIFFRACTIONf_angle_d1.12178487
X-RAY DIFFRACTIONf_dihedral_angle_d19.90322411
X-RAY DIFFRACTIONf_chiral_restr0.0438823
X-RAY DIFFRACTIONf_plane_restr0.0059912
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A15542X-RAY DIFFRACTIONPOSITIONAL
12G15542X-RAY DIFFRACTIONPOSITIONAL0.421
21C1279X-RAY DIFFRACTIONPOSITIONAL
22I1279X-RAY DIFFRACTIONPOSITIONAL0.046
31C1431X-RAY DIFFRACTIONPOSITIONAL
32I1431X-RAY DIFFRACTIONPOSITIONAL0.041
41C1714X-RAY DIFFRACTIONPOSITIONAL
42I1714X-RAY DIFFRACTIONPOSITIONAL0.105
51C5258X-RAY DIFFRACTIONPOSITIONAL
52I5258X-RAY DIFFRACTIONPOSITIONAL0.486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-4.65220.36241690.3493308X-RAY DIFFRACTION84
4.6522-4.70690.37861850.34423526X-RAY DIFFRACTION91
4.7069-4.76430.37771990.34813656X-RAY DIFFRACTION94
4.7643-4.82450.39232070.33283805X-RAY DIFFRACTION97
4.8245-4.8880.37981940.34393853X-RAY DIFFRACTION98
4.888-4.95490.39242090.34453867X-RAY DIFFRACTION99
4.9549-5.02560.38291920.35243847X-RAY DIFFRACTION99
5.0256-5.10050.38122080.34613886X-RAY DIFFRACTION99
5.1005-5.18020.38021930.34213900X-RAY DIFFRACTION99
5.1802-5.2650.35552080.33263906X-RAY DIFFRACTION99
5.265-5.35570.40032280.32863888X-RAY DIFFRACTION100
5.3557-5.45290.35852180.32143893X-RAY DIFFRACTION100
5.4529-5.55770.34892130.31153917X-RAY DIFFRACTION100
5.5577-5.6710.33731770.30413963X-RAY DIFFRACTION100
5.671-5.79410.342040.30413912X-RAY DIFFRACTION100
5.7941-5.92870.35782340.30853904X-RAY DIFFRACTION100
5.9287-6.07670.34321970.30583969X-RAY DIFFRACTION100
6.0767-6.24070.3512050.29233939X-RAY DIFFRACTION100
6.2407-6.4240.32452090.27913941X-RAY DIFFRACTION100
6.424-6.63090.27642050.25213940X-RAY DIFFRACTION100
6.6309-6.86730.30822340.23313973X-RAY DIFFRACTION100
6.8673-7.14150.27212160.21583948X-RAY DIFFRACTION100
7.1415-7.46550.20872230.19293924X-RAY DIFFRACTION100
7.4655-7.85760.21061910.1724028X-RAY DIFFRACTION100
7.8576-8.34780.19872070.14813982X-RAY DIFFRACTION100
8.3478-8.98890.18232130.13834017X-RAY DIFFRACTION100
8.9889-9.88710.15862180.13584022X-RAY DIFFRACTION100
9.8871-11.30320.15492050.13064048X-RAY DIFFRACTION100
11.3032-14.18610.17422160.16364103X-RAY DIFFRACTION100
14.1861-49.81020.32642440.30724272X-RAY DIFFRACTION100

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