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- PDB-4roe: Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter -

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Basic information

Entry
Database: PDB / ID: 4roe
TitleHuman TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 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 transcription factor SL1 complex / regulation of transcription by RNA polymerase III / RNA polymerase III general transcription initiation factor activity / 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 transcription factor SL1 complex / regulation of transcription by RNA polymerase III / RNA polymerase III general transcription initiation factor activity / 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 / RNA Polymerase I Transcription Termination / transcription preinitiation complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 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 / TFIIB-class transcription factor binding / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / 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 / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / euchromatin / 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
: / BRF2-like, C-terminal cyclin repeat / TATA-Binding Protein / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-Binding Protein / TATA-box binding protein, eukaryotic ...: / BRF2-like, C-terminal cyclin repeat / TATA-Binding Protein / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Cyclin-like / Zinc finger, TFIIB-type / TFIIB zinc-binding / TATA-Binding Protein / TATA-box binding protein, eukaryotic / 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: 2.2 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)78,0566
Polymers78,0074
Non-polymers492
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-51 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.741, 91.926, 102.423
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


Mass: 8525.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide / Source: (synth.) synthetic construct (others)
#4: DNA chain Non-template strand


Mass: 8680.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 314 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
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: 2.2→30 Å / Num. obs: 37886 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 59.17 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.617 / Mean I/σ(I) obs: 0.8 / Num. unique all: 5382 / % possible all: 98.7

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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: 2.2→29.68 Å / Cor.coef. Fo:Fc: 0.9556 / Cor.coef. Fo:Fc free: 0.9452 / SU R Cruickshank DPI: 0.234 / 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
Rfree0.2217 1895 5.01 %RANDOM
Rwork0.1919 ---
obs0.1934 37832 99.73 %-
Displacement parametersBiso mean: 73.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.9806 Å20 Å20 Å2
2---5.2396 Å20 Å2
3---0.259 Å2
Refine analyzeLuzzati coordinate error obs: 0.357 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 1084 2 312 5234
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015130HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17170HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2131SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes619HARMONIC5
X-RAY DIFFRACTIONt_it5130HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion3.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion671SEMIHARMONIC5
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_contact5679SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2566 132 4.64 %
Rwork0.2296 2713 -
all0.2309 2845 -
obs--99.73 %
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)
16.0475-0.2032-0.17292.76691.00671.65220.0991-0.00940.5442-0.20550.1073-0.54420.12340.5442-0.2064-0.19490.04030.11880.0025-0.0780.02621.3576-0.61414.5022
22.04460.29121.17520.88490.482.83170.1389-0.15270.0475-0.01030.0120.0590.0095-0.4148-0.1509-0.18410.0112-0.0167-0.0008-0.0436-0.0688-28.7531-17.27436.2638
30.68992.1231-1.178500.53480.43710.0044-0.0313-0.0494-0.0271-0.01910.07850.02210.00380.01470.1146-0.0076-0.09660.18410.03110.0816-10.3073-25.720943.5199
41.52221.73721.849101.871.263-0.0224-0.4364-0.4870.4913-0.0712-0.3141-0.2225-0.05020.09360.2005-0.0086-0.1045-0.12720.0424-0.263113.3325-31.129648.56
51.2732-2.8615-2.57141.02430.73690.27820.00970.0740.1267-0.32130.017-0.0868-0.03640.1037-0.0268-0.0895-0.0628-0.02810.03890.14660.070124.6346-43.739931.1303
63.6938-1.52051.40471.8395-0.71.8148-0.2919-0.23720.30570.4380.0521-0.154-0.2193-0.1210.2397-0.0196-0.135-0.0241-0.0971-0.0696-0.15412.4906-14.9634.8154
70.4520.27860.28880.5342-0.33920.56380.00330.0180.0063-0.00910.00380.0044-0.0077-0.0219-0.0070.15250.0153-0.09410.117-0.07620.0752-17.1952-39.79017.4445
80.067-0.3845-0.94758.19460.68996.8090.13680.2128-0.5442-0.1038-0.1814-0.06050.54420.47340.0446-0.25030.041-0.152-0.2073-0.1365-0.0243-6.0113-25.455219.7692
93.7234-0.41-1.47511.64911.25275.54670.06670.33810.5442-0.5413-0.0521-0.5442-0.5310.5336-0.0147-0.0398-0.13080.066-0.11110.12610.023918.9095-7.549719.7032
100.9835-0.4045-0.48380.5331-0.19290.1510.0022-0.02010.02210.0316-0.00210.01590.06690.0226-0.0001-0.049-0.00440.1520.09770.0243-0.033833.0043-2.08513.079
113.5173-0.3073-2.69591.69530.92377.0230.1721-0.01290.5442-0.29090.0377-0.3404-0.54420.1793-0.2098-0.1219-0.06330.0617-0.0890.0023-0.036514.527-11.453121.5071
121.20120.1423-0.44190.497-2.90850.02980.063-0.1264-0.5442-0.4845-0.14420.2320.5442-0.20040.08110.0384-0.0314-0.0959-0.1201-0.13640.0941-9.5516-30.447117.8662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|64 - A|167 }A64 - 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|411 }A396 - 411
6X-RAY DIFFRACTION6{ B|158 - B|334 }B158 - 334
7X-RAY DIFFRACTION7{ N|3 - N|5 }N3 - 5
8X-RAY DIFFRACTION8{ N|6 - N|14 }N6 - 14
9X-RAY DIFFRACTION9{ N|15 - N|28 }N15 - 28
10X-RAY DIFFRACTION10{ T|2 - T|4 }T2 - 4
11X-RAY DIFFRACTION11{ T|5 - T|14 }T5 - 14
12X-RAY DIFFRACTION12{ T|15 - T|28 }T15 - 28

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