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Basic information

Entry
Database: PDB / ID: 3mlq
TitleCrystal structure of the Thermus thermophilus transcription-repair coupling factor RNA polymerase interacting domain with the Thermus aquaticus RNA polymerase beta1 domain
Components
  • DNA-directed RNA polymerase subunit beta
  • Transcription-repair coupling factor
KeywordsTRANSFERASE/TRANSCRIPTION / Tudor / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


transcription-coupled nucleotide-excision repair, DNA damage recognition / DNA-directed RNA polymerase complex / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / damaged DNA binding / hydrolase activity / DNA-templated transcription ...transcription-coupled nucleotide-excision repair, DNA damage recognition / DNA-directed RNA polymerase complex / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / damaged DNA binding / hydrolase activity / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / ATP binding / cytoplasm
Similarity search - Function
: / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain ...: / Transcription-repair coupling factor / Transcription-repair-coupling factor, C-terminal domain / TRCF-like, C-terminal D7 domain / TRCF domain / TRCF / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / Thrombin, subunit H - #170 / 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 / DNA-directed RNA polymerase beta subunit, bacterial-type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Transcription-repair-coupling factor / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsDarst, S.A. / Westblade, L.F. / Campbell, E.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction.
Authors: Westblade, L.F. / Campbell, E.A. / Pukhrambam, C. / Padovan, J.C. / Nickels, B.E. / Lamour, V. / Darst, S.A.
History
DepositionApr 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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 beta
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta
E: Transcription-repair coupling factor
F: Transcription-repair coupling factor
G: Transcription-repair coupling factor
H: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4289
Polymers116,3338
Non-polymers951
Water00
1
A: DNA-directed RNA polymerase subunit beta
E: Transcription-repair coupling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1783
Polymers29,0832
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-directed RNA polymerase subunit beta
F: Transcription-repair coupling factor


Theoretical massNumber of molelcules
Total (without water)29,0832
Polymers29,0832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA-directed RNA polymerase subunit beta
G: Transcription-repair coupling factor


Theoretical massNumber of molelcules
Total (without water)29,0832
Polymers29,0832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA-directed RNA polymerase subunit beta
H: Transcription-repair coupling factor


Theoretical massNumber of molelcules
Total (without water)29,0832
Polymers29,0832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.585, 106.585, 122.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERAA17 - 3922 - 185
21PROPROSERSERBB17 - 3922 - 185
31PROPROSERSERCC17 - 3922 - 185
41PROPROSERSERDD17 - 3922 - 185
12GLNGLNLEULEUEE334 - 36818 - 52
22GLNGLNLEULEUFF334 - 36818 - 52
32GLNGLNLEULEUGG334 - 36818 - 52
42GLNGLNLEULEUHH334 - 36818 - 52

NCS ensembles :
ID
1
2

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Components

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


Mass: 21081.096 Da / Num. of mol.: 4 / Fragment: beta1 domain (UNP residues 17-139 and 334-395)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: rpoB / Plasmid: pET21a-based / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#2: Protein
Transcription-repair coupling factor


Mass: 8002.165 Da / Num. of mol.: 4
Fragment: RNA polymerase interacting domain (UNP residues 321-387)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: mfd, TT_C0533 / Plasmid: pET21a-based / Production host: Escherichia coli (E. coli) / References: UniProt: Q72KB4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris-HCl, 1.6 M di-potassium ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.522
11-H, K, -L20.478
ReflectionResolution: 2.9→30 Å / Num. all: 27972 / Num. obs: 25538 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.8 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Thermus aquaticus RNA polymerase beta-subunit beta1 domain

Resolution: 2.91→29.56 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.907 / SU B: 29.72 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24983 1170 4.4 %RANDOM
Rwork0.22691 ---
obs0.22792 25538 88.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.019 Å2
Baniso -1Baniso -2Baniso -3
1--14.19 Å20 Å20 Å2
2---14.19 Å20 Å2
3---28.39 Å2
Refinement stepCycle: LAST / Resolution: 2.91→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6858 0 5 0 6863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226980
X-RAY DIFFRACTIONr_bond_other_d0.0020.024902
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9979416
X-RAY DIFFRACTIONr_angle_other_deg0.906311897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8135867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94423.591323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.464151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8851565
X-RAY DIFFRACTIONr_chiral_restr0.0960.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
X-RAY DIFFRACTIONr_mcbond_it0.2671.54371
X-RAY DIFFRACTIONr_mcbond_other0.0421.51796
X-RAY DIFFRACTIONr_mcangle_it0.48526977
X-RAY DIFFRACTIONr_scbond_it0.42932609
X-RAY DIFFRACTIONr_scangle_it0.7274.52439
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1024MEDIUM POSITIONAL0.350.5
12B1024MEDIUM POSITIONAL0.360.5
13C1024MEDIUM POSITIONAL0.330.5
14D1024MEDIUM POSITIONAL0.330.5
11A1309LOOSE POSITIONAL0.895
12B1309LOOSE POSITIONAL1.055
13C1309LOOSE POSITIONAL0.825
14D1309LOOSE POSITIONAL0.955
11A1024MEDIUM THERMAL0.142
12B1024MEDIUM THERMAL0.132
13C1024MEDIUM THERMAL0.132
14D1024MEDIUM THERMAL0.132
11A1309LOOSE THERMAL0.1910
12B1309LOOSE THERMAL0.1910
13C1309LOOSE THERMAL0.1910
14D1309LOOSE THERMAL0.1810
21E109MEDIUM POSITIONAL0.520.5
22F109MEDIUM POSITIONAL0.480.5
23G109MEDIUM POSITIONAL0.410.5
24H109MEDIUM POSITIONAL0.550.5
21E165LOOSE POSITIONAL1.035
22F165LOOSE POSITIONAL1.195
23G165LOOSE POSITIONAL0.955
24H165LOOSE POSITIONAL0.935
21E109MEDIUM THERMAL0.362
22F109MEDIUM THERMAL0.342
23G109MEDIUM THERMAL0.372
24H109MEDIUM THERMAL1.022
21E165LOOSE THERMAL0.1810
22F165LOOSE THERMAL0.1710
23G165LOOSE THERMAL0.1810
24H165LOOSE THERMAL0.3910
LS refinement shellResolution: 2.908→2.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 74 -
Rwork0.274 1476 -
obs--70.42 %
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)
13.03690.5571-0.43381.8885-0.76161.69660.0044-0.0598-0.1528-0.03640.0008-0.01270.13890.1374-0.00530.02930.005-0.03090.0401-0.01840.1693121.96615.17273.978
22.08250.20.63591.72310.2050.67120.0171-0.22260.19320.0655-0.0872-0.0108-0.15330.02910.070.0771-0.01550.01260.08630.0060.1836108.4637.35767.738
32.29490.9586-1.28392.7856-0.73182.4673-0.0189-0.0366-0.01570.04530.03380.00110.1386-0.0262-0.01490.05190.011-0.01870.0082-0.0190.1558144.29737.52899.38
42.17250.79980.28412.57390.63080.90630.00910.1188-0.1297-0.18590.04040.1290.0829-0.0998-0.04940.09490.0218-0.020.06140.0040.1834122.50151.549105.627
53.3704-2.62170.49127.9022-0.00945.4293-0.07550.0385-0.19420.28050.0529-0.54330.21570.10070.02270.1944-0.0589-0.05940.3101-0.01510.395996.7894.56577.649
64.1128-0.83632.08565.1306-2.23136.83670.0248-0.10850.3951-0.17610.09220.0619-0.31820.6913-0.11710.0653-0.0010.01580.4184-0.06910.5129135.26346.8966.945
78.2925-0.9877-2.31163.27410.52245.4905-0.20150.0222-0.20040.36820.1745-0.2120.0240.51510.0270.3125-0.0489-0.02350.1318-0.0870.3512153.89563.35195.649
88.9398-1.5140.42193.871-3.28143.4978-0.20880.25770.06690.13740.41340.46-0.4832-0.2218-0.20450.3437-0.08390.03840.20760.02770.5036110.70825.681105.736
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 394
2X-RAY DIFFRACTION2B17 - 392
3X-RAY DIFFRACTION3C17 - 394
4X-RAY DIFFRACTION4D16 - 393
5X-RAY DIFFRACTION5E332 - 369
6X-RAY DIFFRACTION6F333 - 369
7X-RAY DIFFRACTION7G329 - 368
8X-RAY DIFFRACTION8H334 - 375

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