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- PDB-4rod: Human TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter -

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Basic information

Entry
Database: PDB / ID: 4rod
TitleHuman TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter
Components
  • Non-template strand
  • TATA-box-binding protein
  • Template strand
  • Transcription factor IIIB 50 kDa subunit
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


transcription preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / regulation of transcription by RNA polymerase III / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter ...transcription preinitiation complex assembly / transcription factor TFIIIB complex / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / regulation of transcription by RNA polymerase III / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / RNA polymerase II general transcription initiation factor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / cellular response to oxidative stress / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
TATA-Binding Protein / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site ...TATA-Binding Protein / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-box binding protein, eukaryotic / TATA-Binding Protein / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Cyclin A; domain 1 / TBP domain superfamily / Cyclin-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / TATA-box-binding protein / Transcription factor IIIB 50 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVannini, A. / Gouge, J. / Satia, K. / Guthertz, N.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2015
Title: Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2.
Authors: Gouge, J. / Satia, K. / Guthertz, N. / Widya, M. / Thompson, A.J. / Cousin, P. / Dergai, O. / Hernandez, N. / Vannini, A.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor IIIB 50 kDa subunit
B: TATA-box-binding protein
N: Template strand
T: Non-template strand


Theoretical massNumber of molelcules
Total (without water)78,0124
Polymers78,0124
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-45 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.040, 91.377, 102.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor IIIB 50 kDa subunit / TFIIIB50 / hTFIIIB50 / B-related factor 2 / BRF-2 / hBRFU


Mass: 40203.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRF2, BRFU, PRO1470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAW0
#2: Protein TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation ...TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 20597.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Escherichia coli (E. coli) / References: UniProt: P20226
#3: DNA chain Template strand


Mass: 8618.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide / Source: (synth.) synthetic construct (others)
#4: DNA chain Non-template strand


Mass: 8592.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2014
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 20256 / % possible obs: 98.9 % / Observed criterion σ(I): 0.9 / Redundancy: 4.8 % / Biso Wilson estimate: 91.66 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 6.9
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 2.212 / Mean I/σ(I) obs: 0.9 / Num. unique all: 2947 / % possible all: 99.4

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Processing

Software
NameVersionClassification
GDA(Generic Data Acquisition)data collection
PHASERphasing
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.65 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9078 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The density between the residues 365 and 374 is very poor, the linker has been built with 0 occupancy
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1039 5.14 %RANDOM
Rwork0.2004 ---
obs0.2028 20221 98.38 %-
Displacement parametersBiso mean: 81.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.4667 Å20 Å20 Å2
2--0.8781 Å20 Å2
3---0.5885 Å2
Refine analyzeLuzzati coordinate error obs: 0.481 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 1122 0 127 5047
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015128HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17174HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2116SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes613HARMONIC5
X-RAY DIFFRACTIONt_it5128HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion3.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion670SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5341SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.85 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2599 147 5 %
Rwork0.2348 2793 -
all0.236 2940 -
obs--98.38 %
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)
18.31550.3333-0.60596.4674-1.68035.08990.2168-0.06980.44410.3253-0.13770.5442-0.2788-0.5442-0.0792-0.19120.02740.152-0.2579-0.0270.0641-1.146-0.8257-4.5822
21.5519-0.29011.38152.1651-0.43913.80450.14560.09530.13730.0676-0.0188-0.39540.01230.4802-0.1269-0.17680.0161-0.0201-0.13590.05140.132828.5397-17.0546-6.1594
30.2198-0.14010.1691.43390.37570.15280.0048-0.0924-0.019-0.0246-0.0155-0.0462-0.01340.07670.01070.1156-0.0383-0.11410.15850.09050.101610.6347-22.8418-43.4222
41.2396-2.91042.78320-2.91045.8234-0.00710.1538-0.0294-0.1113-0.00390.0824-0.0203-0.06030.0110.21150.1033-0.152-0.3002-0.0934-0.0301-12.9083-30.2769-49.2416
51.74722.4327-0.63120.7777-1.59520.2804-0.0233-0.096-0.05860.14250.02810.02890.02670.0065-0.00480.03150.0650.0351-0.0389-0.1520.0643-24.2561-42.8384-34.291
63.67151.82211.76052.31661.32261.9319-0.31640.4360.37-0.54420.08860.3085-0.26480.21320.22780.04530.1168-0.0577-0.23990.08150.009-2.0318-14.0505-35.1903
74.59981.73012.59553.105-0.78080.09120.0258-0.02530.1676-0.05430.1622-0.0882-0.21660.3797-0.18810.27820.152-0.152-0.10460.152-0.165218.6101-35.3604-8.9225
85.77691.39661.83918.2227-2.91048.31550.04060.0413-0.54420.3559-0.07960.09370.5442-0.03890.039-0.10960.152-0.152-0.20680.1520.10534.1922-22.0331-21.5459
95.4839-2.869-2.91044.69882.78647.7606-0.0445-0.14020.54420.54420.28060.5442-0.0985-0.5442-0.2362-0.030.1520.152-0.2179-0.1520.304-21.1029-5.4972-18.5208
102.90112.5444-2.0754.1949-0.785400.0246-0.037-0.0602-0.00850.052-0.0670.2014-0.0915-0.0766-0.11060.1520.1520.1257-0.152-0.1567-32.5239-1.3188-10.503
110.754-0.502-2.91040.35311.49728.31550.0755-0.30870.54290.5442-0.20780.1807-0.5442-0.14350.1323-0.05110.1520.152-0.1947-0.1520.2999-14.073-11.2843-21.9059
122.5737-1.60041.25896.5553-1.66696.60140.15070.2724-0.54420.54420.1255-0.04870.54420.5342-0.2762-0.04210.152-0.1336-0.25270.1520.127610.7595-28.8272-17.4937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|66 - A|167 }A66 - 167
2X-RAY DIFFRACTION2{ A|168 - A|366 }A168 - 366
3X-RAY DIFFRACTION3{ A|367 - A|378 }A367 - 378
4X-RAY DIFFRACTION4{ A|379 - A|395 }A379 - 395
5X-RAY DIFFRACTION5{ A|396 - A|407 }A396 - 407
6X-RAY DIFFRACTION6{ B|158 - B|334 }B158 - 334
7X-RAY DIFFRACTION7{ N|2 - N|5 }N2 - 5
8X-RAY DIFFRACTION8{ N|6 - N|14 }N6 - 14
9X-RAY DIFFRACTION9{ N|15 - N|28 }N15 - 28
10X-RAY DIFFRACTION10{ T|1 - T|4 }T1 - 4
11X-RAY DIFFRACTION11{ T|5 - T|14 }T5 - 14
12X-RAY DIFFRACTION12{ T|15 - T|28 }T15 - 28

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