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- PDB-9v4m: Crystal structure of the T.thermophilus transcription initiation ... -

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Basic information

Entry
Database: PDB / ID: 9v4m
TitleCrystal structure of the T.thermophilus transcription initiation complex bound to Ap4G
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • Non-template DNA Strand
  • RNA polymerase sigma factor SigA
  • Template DNA strand
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / 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 RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal 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. ...: / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / RNA polymerase, RBP11-like subunit / 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 alpha / RNA polymerase sigma factor SigA / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDuan, W. / Kaushik, A. / Serganov, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112904 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21GM151508 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM088118-09 United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Molecular basis for noncanonical transcription initiation from Np4A alarmones
Authors: Duan, W. / Kaushik, A. / Unarta, I.C. / Wu, Y. / Liu, M.M.J. / Weaver, J.W. / Wang, B. / Rice, W.J. / Luciano, D.J. / Belasco, J.G. / Huang, X. / Nudler, E. / Serganov, A.
History
DepositionMay 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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: Template DNA strand
H: Non-template DNA Strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,42517
Polymers444,1008
Non-polymers1,3259
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51780 Å2
ΔGint-226 kcal/mol
Surface area135590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.055, 103.211, 296.509
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

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


Mass: 35056.164 Da / Num. of mol.: 2 / 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 / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 125436.539 Da / Num. of mol.: 1 / 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' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 170997.391 Da / Num. of mol.: 1 / 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 / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 11533.316 Da / Num. of mol.: 1 / 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, 1 molecules F

#5: Protein RNA polymerase sigma factor SigA


Mass: 50900.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: sigA, TTHA0532 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SKW1

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DNA chain , 2 types, 2 molecules GH

#6: DNA chain Template DNA strand


Mass: 6698.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain Non-template DNA Strand


Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 76 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#9: Chemical ChemComp-A1IF9 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 852.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O20P4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 180 mM Kcl, 50 mM Mgcl2, 12.5% PEG4000, 100 mM Tris.Hcl pH 8.7

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 105883 / % possible obs: 95.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 59.92 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.065 / Rrim(I) all: 0.143 / Net I/σ(I): 10.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.24 / Num. unique obs: 10426 / CC1/2: 0.53 / CC star: 0.83 / % possible all: 28.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q5S

4q5s


Resolution: 3→29.96 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 2024 2.33 %
Rwork0.2791 --
obs0.2793 86969 78.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26463 755 76 67 27361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727890
X-RAY DIFFRACTIONf_angle_d0.90937891
X-RAY DIFFRACTIONf_dihedral_angle_d10.6924128
X-RAY DIFFRACTIONf_chiral_restr0.0624267
X-RAY DIFFRACTIONf_plane_restr0.0094831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.3799500.36452086X-RAY DIFFRACTION27
3.07-3.160.3282730.34542955X-RAY DIFFRACTION38
3.16-3.250.38681090.34053954X-RAY DIFFRACTION52
3.25-3.350.34241030.32954756X-RAY DIFFRACTION62
3.35-3.470.34051360.33575467X-RAY DIFFRACTION71
3.47-3.610.31291460.32786178X-RAY DIFFRACTION80
3.61-3.780.30941610.31436877X-RAY DIFFRACTION89
3.78-3.980.35251840.29587192X-RAY DIFFRACTION94
3.98-4.220.31381680.2847388X-RAY DIFFRACTION95
4.22-4.550.24191730.2647446X-RAY DIFFRACTION96
4.55-50.26521740.26247504X-RAY DIFFRACTION97
5-5.720.30891800.2737522X-RAY DIFFRACTION97
5.72-7.20.31651800.27427776X-RAY DIFFRACTION99
7.2-29.960.20471870.22397844X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8618-0.1573-0.21540.34140.20180.6964-0.01830.06070.08560.070.0419-0.0562-0.03170.33870.01160.4655-0.1689-0.06930.7633-0.0740.23818.86419.7679122.0885
20.74860.0299-0.08360.51650.00760.5732-0.0667-0.00770.1940.02990.10430.0391-0.3411-0.1076-0.04330.77320.02590.10560.2197-0.03860.3866-22.779422.7575127.6627
30.3223-0.0873-0.08590.31650.07570.4188-0.05620.0886-0.1253-0.04170.1018-0.07090.20041.0246-0.02640.36340.34640.00260.855-0.11340.3215.1991-12.70279.3235
40.4493-0.2612-0.11230.28330.00871.22180.13281.01330.0370.0084-0.17120.2379-0.13420.8410.06290.2394-0.1314-0.0543-0.0256-0.38530.2458-8.06653.047861.688
50.91660.48190.07080.97460.27530.0817-0.02580.06710.324-0.0244-0.0057-0.1127-0.28840.19560.03190.8772-0.2188-0.01460.352-0.08470.4438-12.017141.198982.2099
60.23160.0365-0.04050.20990.1050.21290.1150.14650.1578-0.0308-0.1402-0.0511-0.09970.0791-0.00330.56050.03030.01141.0959-0.03510.617230.870310.989740.8608
70.8717-0.2642-0.89511.6616-0.21851.06790.12120.2114-0.2851-0.13240.0917-0.09680.19920.2001-0.21380.4482-0.00710.07870.62-0.05890.6062-0.2107-4.331761.4032
80.6188-0.0289-0.5744-0.01080.02940.5344-0.0660.00560.0551-0.0135-0.0298-0.070.11780.14670.07930.95630.04130.00211.1241-0.03811.050313.0017-15.232242.9341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 230)
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 229)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 1118)
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 1499)
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 95)
6X-RAY DIFFRACTION6(chain 'F' and resid 77 through 423)
7X-RAY DIFFRACTION7(chain 'G' and resid 6 through 20)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 22)

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