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- PDB-4roc: Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter -

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Basic information

Entry
Database: PDB / ID: 4roc
TitleHuman TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter
Components
  • Non-template strandCoding strand
  • TATA-box-binding protein
  • Template strandTranscription (biology)
  • 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 / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / RNA polymerase II general transcription initiation factor activity / transcription by RNA polymerase III / 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 / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / 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 / metal ion binding / nucleus / 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: 1.9 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 1.1Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0335
Polymers78,0094
Non-polymers241
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-55 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.276, 89.911, 102.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#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

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DNA chain , 2 types, 2 molecules NT

#3: DNA chain Template strand / Transcription (biology)


Mass: 8757.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide / Source: (synth.) synthetic construct (others)
#4: DNA chain Non-template strand / Coding strand


Mass: 8450.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 380 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
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: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.9→29.51 Å / Num. obs: 56530 / % possible obs: 99.3 % / Observed criterion σ(I): 0.5 / Redundancy: 4.2 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 3.193 / Mean I/σ(I) obs: 0.5 / Num. unique all: 8147 / % possible all: 99.3

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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
Starting model: 1C9B

1c9b


Resolution: 1.9→29.51 Å / Cor.coef. Fo:Fc: 0.9638 / Cor.coef. Fo:Fc free: 0.9515 / SU R Cruickshank DPI: 0.137 / 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
Rfree0.2152 2797 4.96 %RANDOM
Rwork0.1857 ---
obs0.1872 56427 99.14 %-
Displacement parametersBiso mean: 62.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.1657 Å20 Å20 Å2
2--0.1963 Å20 Å2
3----0.0306 Å2
Refine analyzeLuzzati coordinate error obs: 0.312 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 1101 1 379 5286
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015133HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.957184HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2128SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes619HARMONIC5
X-RAY DIFFRACTIONt_it5133HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion3.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion673SEMIHARMONIC5
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_contact5738SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2837 203 4.99 %
Rwork0.2741 3869 -
all0.2746 4072 -
obs--99.14 %
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)
16.1834-1.7641-0.94483.51120.20592.01510.16370.4633-0.5442-0.5442-0.18590.53050.072-0.35420.0222-0.0884-0.0126-0.0814-0.1001-0.0316-0.0494-0.58670.59274.4123
21.84550.3594-1.17261.0887-0.252.52550.0367-0.1436-0.0508-0.0470.0365-0.169-0.02420.3168-0.0731-0.1370.00630.0586-0.04670.0293-0.003429.060716.84366.3204
31.7810.34771.44011.0190.66410.1603-0.0004-0.0745-0.0040.0505-0.00270.00260.0036-0.02890.00320.0709-0.0005-0.00760.12750.00620.07269.61124.712442.5352
402.9104-0.84490-2.58522.8543-0.0882-0.31440.12960.4594-0.08250.19280.3221-0.01380.17080.17150.06390.152-0.1366-0.0047-0.2231-13.75829.200549.0093
51.9661-2.9104-0.46671.3592-2.91040.8209-0.08470.0141-0.1479-0.18550.13020.1802-0.0053-0.0852-0.0455-0.0528-0.03730.0738-0.0317-0.11010.1215-24.671641.775733.739
61.8306-1.0453-0.84931.87460.78861.2866-0.1783-0.2466-0.20840.42460.04830.19820.13730.14430.1299-0.0175-0.03980.0651-0.10610.0715-0.1162-1.912313.311435.0497
71.2289-0.0772-0.8761.3320.34330.26570.0029-0.0195-0.03530.03110.0348-0.02250.06630.0605-0.03770.0955-0.10050.1520.08250.1510.008419.288534.054410.1485
80.6854-2.1593-2.81183.894-2.91048.28290.12510.19170.5442-0.13770.08410.0537-0.5442-0.2856-0.2092-0.2507-0.01930.0112-0.23510.152-0.06944.21621.306421.3501
91.2208-0.12910.07650-0.78942.69340.04830.415-0.5442-0.1009-0.03080.54420.5394-0.5442-0.0176-0.0844-0.0831-0.0492-0.0132-0.1520.2785-20.7575.087817.9394
100.9197-0.23660.23451.89570.38030.23060.0046-0.0481-0.0153-0.00610.00690.0043-0.0132-0.0013-0.01150.088-0.0151-0.1520.0715-0.05510.0294-33.07990.582410.3785
110.288-1.88030.53180-0.18724.160.11230.0455-0.54420.16930.10520.37240.1307-0.1561-0.2175-0.2062-0.0265-0.0297-0.12430.00520.014-14.018310.42421.4358
122.0452-0.1470.3450.62872.47271.4830.04940.05950.5442-0.44380.0694-0.2445-0.54420.3769-0.11880.0599-0.03940.1327-0.12730.10550.05729.976927.388818.1238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|65 - A|167 }A65 - 167
2X-RAY DIFFRACTION2{ A|168 - A|364 }A168 - 364
3X-RAY DIFFRACTION3{ A|375 - A|378 }A375 - 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|27 }T15 - 27

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