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

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Basic information

Entry
Database: PDB / ID: 4xlr
TitleCrystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA
Components
  • (DNA (48-MER)) x 2
  • (DNA-directed RNA polymerase subunit ...) x 4
  • CarD-like transcriptional regulator
  • RNA (5'-R(P*UP*CP*GP*A)-3')
  • 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 / rRNA transcription / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : ...sigma factor activity / rRNA transcription / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
CarD-like, C-terminal domain / : / : / CarD, C-terminal domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain ...CarD-like, C-terminal domain / : / : / CarD, C-terminal domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / : / 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 / 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 Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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) / RNA / CarD-like transcriptional regulator / 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)
Thermus thermophilus JL-18 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.3 Å
AuthorsBae, B. / Darst, S.A.
CitationJournal: Elife / Year: 2015
Title: CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
Authors: Bae, B. / Chen, J. / Davis, E. / Leon, K. / Darst, S.A. / Campbell, E.A.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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
M: CarD-like transcriptional regulator
N: CarD-like transcriptional regulator
O: DNA (48-MER)
P: DNA (48-MER)
Q: RNA (5'-R(P*UP*CP*GP*A)-3')
R: DNA (48-MER)
S: DNA (48-MER)
T: RNA (5'-R(P*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)933,41726
Polymers933,10720
Non-polymers3106
Water00
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
M: CarD-like transcriptional regulator
O: DNA (48-MER)
P: DNA (48-MER)
Q: RNA (5'-R(P*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,70913
Polymers466,55310
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
N: CarD-like transcriptional regulator
R: DNA (48-MER)
S: DNA (48-MER)
T: RNA (5'-R(P*UP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,70913
Polymers466,55310
Non-polymers1553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)289.840, 289.840, 536.340
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

NCS oper:
IDCodeMatrixVector
1given(0.639845, -0.768447, 0.009352), (-0.768204, -0.639888, -0.02017), (0.021484, 0.005721, -0.999753)109.448997, 237.033005, 175.707001
2given(0.632655, -0.774425, 0.003785), (-0.774263, -0.63261, -0.017916), (0.016269, 0.008404, -0.999832)111.578003, 236.054001, 175.759003
3given(0.641787, -0.766693, 0.01704), (-0.766282, -0.642006, -0.02531), (0.030345, 0.003187, -0.999534)108.626999, 237.608994, 175.492004
4given(0.652916, -0.7572, 0.018657), (-0.756169, -0.653052, -0.041611), (0.043692, 0.01306, -0.99896)105.557999, 240.800995, 172.774994
5given(0.642789, -0.765816, 0.018691), (-0.765129, -0.643022, -0.033162), (0.037414, 0.007015, -0.999275)108.038002, 238.647003, 174.746994

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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 / 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 / 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' / 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 / 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 , 2 types, 4 molecules FLMN

#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
#6: Protein CarD-like transcriptional regulator


Mass: 18316.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_0238 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9ZP94

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DNA chain , 2 types, 4 molecules ORPS

#7: DNA chain DNA (48-MER)


Mass: 14878.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA non-template strand / Source: (synth.) synthetic construct (others)
#8: DNA chain DNA (48-MER)


Mass: 14831.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 2 molecules QT

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


Mass: 1240.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA transcript / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 6 molecules

#10: Chemical
ChemComp-ZN / ZINC ION


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


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

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Details

Has protein modificationY

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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: 6.03 Å3/Da / Density % sol: 79.61 %
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: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 4.15→40 Å / Num. obs: 171617 / % possible obs: 97.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 165.1 Å2 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.137 / Rrim(I) all: 0.222 / Χ2: 1.869 / Net I/av σ(I): 3.314 / Net I/σ(I): 2 / Num. measured all: 1302221
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
4.15-4.34.8129290.0281.4873.9
4.3-4.476.1173210.0621.5699.3
4.47-4.676.5174160.0941.5699.6
4.67-4.927175140.1491.57299.9
4.92-5.237.5175590.1391.591100
5.23-5.638.2175600.2131.61299.9
5.63-6.198.7176140.291.62899.80.894
6.19-7.099176890.5271.68399.70.534
7.09-8.918.9177920.9452.13999.50.1650.4690.498
8.91-408.2182230.9933.33498.70.0480.1330.142

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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
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.3→39.562 Å / SU ML: 1.01 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.31 7333 5 %
Rwork0.275 --
obs0.2767 146529 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.3→39.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56732 4116 6 0 60854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00562398
X-RAY DIFFRACTIONf_angle_d0.95985213
X-RAY DIFFRACTIONf_dihedral_angle_d19.89924290
X-RAY DIFFRACTIONf_chiral_restr0.0379564
X-RAY DIFFRACTIONf_plane_restr0.00510467
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A15542X-RAY DIFFRACTIONPOSITIONAL
12G15542X-RAY DIFFRACTIONPOSITIONAL0.013
21C1302X-RAY DIFFRACTIONPOSITIONAL
22I1302X-RAY DIFFRACTIONPOSITIONAL0.008
31C1431X-RAY DIFFRACTIONPOSITIONAL
32I1431X-RAY DIFFRACTIONPOSITIONAL0.009
41C1714X-RAY DIFFRACTIONPOSITIONAL
42I1714X-RAY DIFFRACTIONPOSITIONAL0.013
51C5258X-RAY DIFFRACTIONPOSITIONAL
52I5258X-RAY DIFFRACTIONPOSITIONAL0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3-4.34880.4291960.39863779X-RAY DIFFRACTION78
4.3488-4.39990.42532060.39284094X-RAY DIFFRACTION84
4.3999-4.45350.3882130.38314253X-RAY DIFFRACTION88
4.4535-4.50980.40372090.37444243X-RAY DIFFRACTION88
4.5098-4.5690.39672230.3834361X-RAY DIFFRACTION90
4.569-4.63150.39072320.38224416X-RAY DIFFRACTION91
4.6315-4.69760.41032470.38714472X-RAY DIFFRACTION92
4.6976-4.76760.43792090.36684455X-RAY DIFFRACTION91
4.7676-4.8420.41012470.37574482X-RAY DIFFRACTION93
4.842-4.92120.37252260.36934496X-RAY DIFFRACTION92
4.9212-5.00590.41022480.37544523X-RAY DIFFRACTION93
5.0059-5.09680.4132480.37274584X-RAY DIFFRACTION95
5.0968-5.19460.39322580.37114603X-RAY DIFFRACTION95
5.1946-5.30040.42252560.35854642X-RAY DIFFRACTION96
5.3004-5.41530.38682370.35554686X-RAY DIFFRACTION96
5.4153-5.5410.38662490.37214738X-RAY DIFFRACTION97
5.541-5.67920.41592540.36184746X-RAY DIFFRACTION97
5.6792-5.83230.39912310.33844761X-RAY DIFFRACTION97
5.8323-6.00330.39022550.344765X-RAY DIFFRACTION98
6.0033-6.19640.38962350.32174834X-RAY DIFFRACTION98
6.1964-6.41690.3592390.30994873X-RAY DIFFRACTION99
6.4169-6.67270.36092930.28974793X-RAY DIFFRACTION99
6.6727-6.97480.32322820.26814849X-RAY DIFFRACTION99
6.9748-7.34040.29292540.25744912X-RAY DIFFRACTION99
7.3404-7.7970.27432460.2234926X-RAY DIFFRACTION100
7.797-8.39370.22222580.18594915X-RAY DIFFRACTION99
8.3937-9.22870.20482590.17254939X-RAY DIFFRACTION99
9.2287-10.54190.19812800.16194936X-RAY DIFFRACTION99
10.5419-13.19930.19132430.1555011X-RAY DIFFRACTION98
13.1993-39.5640.25913000.24925109X-RAY DIFFRACTION98

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