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- PDB-5wh1: Apo form of the C-terminal region of human Transcription Factor IIB -

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Basic information

Entry
Database: PDB / ID: 5wh1
TitleApo form of the C-terminal region of human Transcription Factor IIB
ComponentsTranscription initiation factor IIB
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex ...positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / germinal vesicle / nuclear thyroid hormone receptor binding / transcription preinitiation complex / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II complex binding / protein acetylation / 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 / viral transcription / acetyltransferase activity / RNA polymerase II transcribes snRNA genes / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / promoter-specific chromatin binding / protein-DNA complex / transcription initiation at RNA polymerase II promoter / kinetochore / RNA polymerase II transcription regulator complex / chromosome / DNA-binding transcription factor binding / transcription by RNA polymerase II / nuclear body / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Transcription initiation factor IIB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsBratkowski, M.A. / Liu, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114576 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121662 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk.
Authors: Bratkowski, M. / Unarta, I.C. / Zhu, L. / Shubbar, M. / Huang, X. / Liu, X.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor IIB
B: Transcription initiation factor IIB
C: Transcription initiation factor IIB
D: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,51130
Polymers94,0134
Non-polymers2,49826
Water0
1
A: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9846
Polymers23,5031
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9846
Polymers23,5031
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2729
Polymers23,5031
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2729
Polymers23,5031
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.165, 126.461, 158.430
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 initiation factor IIB / General transcription factor TFIIB / S300-II


Mass: 23503.354 Da / Num. of mol.: 4 / Fragment: C-terminal residues 107-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4

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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: 5.76 Å3/Da / Density % sol: 78.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate trihydrate pH 4.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.39→49.73 Å / Num. obs: 30686 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 81.99 Å2 / CC1/2: 0.865 / Rmerge(I) obs: 0.239 / Net I/σ(I): 9.15
Reflection shellResolution: 3.394→3.46 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 30686 / CC1/2: 0.546 / Rpim(I) all: 0.96 / % possible all: 97.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9B

1c9b


Resolution: 3.39→49.73 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.831 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.818 / SU Rfree Blow DPI: 0.331 / SU Rfree Cruickshank DPI: 0.336
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1511 4.92 %RANDOM
Rwork0.194 ---
obs0.195 30686 99.6 %-
Displacement parametersBiso mean: 104.3 Å2
Baniso -1Baniso -2Baniso -3
1--28.4775 Å20 Å20 Å2
2--27.9988 Å20 Å2
3---0.4787 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: 1 / Resolution: 3.39→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6510 0 130 0 6640
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016709HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.249060HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2408SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes156HARMONIC2
X-RAY DIFFRACTIONt_gen_planes955HARMONIC5
X-RAY DIFFRACTIONt_it6709HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion22.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
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_contact8203SEMIHARMONIC4
LS refinement shellResolution: 3.39→3.51 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2569 152 5.29 %
Rwork0.2466 2724 -
all0.2471 2876 -
obs--96.61 %
Refinement TLS params.Method: refined / Origin x: -12.9024 Å / Origin y: 117.093 Å / Origin z: 42.5011 Å
111213212223313233
T0.0062 Å20.0201 Å2-0.0666 Å2--0.2955 Å20.0299 Å2---0.2491 Å2
L1.1627 °20.0245 °2-0.236 °2-2.1123 °20.3892 °2--0.5661 °2
S0.0624 Å °-0.0699 Å °0.0155 Å °-0.0163 Å °0.0243 Å °0.1644 Å °0.0062 Å °-0.0465 Å °-0.0867 Å °
Refinement TLS groupSelection details: { *|* }

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