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- PDB-5gpy: Crystal structure of the human TFIIE complex -

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Basic information

Entry
Database: PDB / ID: 5gpy
TitleCrystal structure of the human TFIIE complex
Components
  • General transcription factor IIE subunit 1
  • Transcription initiation factor IIE subunit beta
KeywordsTRANSCRIPTION / general transcription factor / RNA Polymerase II
Function / homology
Function and homology information


transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 ...transcription factor TFIIE complex / transcription open complex formation at RNA polymerase II promoter / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 II transcribes snRNA genes / RNA Polymerase II Pre-transcription Events / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / molecular adaptor activity / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain ...Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Zinc finger, TFIIB-type / TFIIB zinc-binding / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
General transcription factor IIE subunit 1 / Transcription initiation factor IIE subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsObita, T. / Miwa, K. / Kojima, R. / Ohkuma, Y. / Tamura, Y. / Mizuguchi, M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Crystal Structure of Human General Transcription Factor TFIIE at Atomic Resolution
Authors: Miwa, K. / Kojima, R. / Obita, T. / Ohkuma, Y. / Tamura, Y. / Mizuguchi, M.
History
DepositionAug 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription factor IIE subunit 1
B: Transcription initiation factor IIE subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1363
Polymers38,0712
Non-polymers651
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-32 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.520, 69.200, 116.530
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 General transcription factor IIE subunit 1 / General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha ...General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha / TFIIE-alpha


Mass: 25542.270 Da / Num. of mol.: 1 / Fragment: UNP residues 1-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083
#2: Protein Transcription initiation factor IIE subunit beta / TFIIE-beta / General transcription factor IIE subunit 2


Mass: 12528.278 Da / Num. of mol.: 1 / Fragment: UNP residues 141-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E2, TF2E2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29084
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.73 Å3/Da / Density % sol: 55 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9 / Details: 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.282446 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282446 Å / Relative weight: 1
ReflectionResolution: 2.1→59.5 Å / Num. obs: 24970 / % possible obs: 99.9 % / Redundancy: 3.5 % / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.325 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2372 1291 5.17 %
Rwork0.1985 --
obs0.2007 24970 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 1 77 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082324
X-RAY DIFFRACTIONf_angle_d1.0063118
X-RAY DIFFRACTIONf_dihedral_angle_d14.382903
X-RAY DIFFRACTIONf_chiral_restr0.04346
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.18410.3081500.29422572X-RAY DIFFRACTION100
2.1841-2.28350.36631390.27422569X-RAY DIFFRACTION100
2.2835-2.40390.2981380.25552605X-RAY DIFFRACTION100
2.4039-2.55440.28011440.23282604X-RAY DIFFRACTION100
2.5544-2.75160.24711550.21982592X-RAY DIFFRACTION100
2.7516-3.02850.31061320.22712650X-RAY DIFFRACTION100
3.0285-3.46650.25141370.20262654X-RAY DIFFRACTION100
3.4665-4.36670.19851420.16542665X-RAY DIFFRACTION100
4.3667-41.33260.19511540.17162768X-RAY DIFFRACTION99
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)
12.46520.11460.14434.2505-2.23529.3211-0.0075-0.26420.14230.05880.0599-0.1384-0.0999-0.0117-0.06620.2166-0.003-0.0090.2975-0.04890.237945.804521.239917.8983
21.97273.9123-2.36918.4881-5.24593.50740.03730.0824-0.01770.04060.0610.0112-0.21950.1952-0.05970.4889-0.09190.01570.5289-0.08320.331454.189833.416917.6306
37.5141.4849-1.67193.0269-0.52314.6067-0.04-0.4147-0.10580.3485-0.12980.11-0.0969-0.11850.16240.56990.054-0.06830.4284-0.04360.286740.757314.546141.272
48.53070.4014-3.52063.2026-2.79563.5889-0.1971.1983-1.0237-0.4611-0.2517-0.19671.0922-0.08740.48790.8064-0.07960.10110.8248-0.19460.460817.7349.143561.0901
58.4173-3.815-2.17095.1913.87782.9228-0.27320.2201-0.98220.4801-0.4211.55281.3782-1.45510.69910.8916-0.30850.07960.7088-0.17890.654411.90495.344564.2788
63.8069-1.7484-5.77893.17851.55859.2612-0.542-0.7067-0.80120.00510.2765-0.19051.1920.81210.31520.62640.10360.02290.43670.01290.358944.43335.513334.5046
77.6932.99554.7675.91012.08267.3255-0.14340.7243-0.1163-0.43170.2881-0.20370.0361-0.0116-0.1590.2701-0.00920.06490.42140.00890.234139.250213.1668-1.4326
80.75331.62230.152.8331-0.12967.47160.1136-0.2458-0.03970.1505-0.0440.14380.3858-0.641-0.07970.2747-0.01840.03150.551-0.01960.352134.481712.80910.4925
97.96771.0028-0.89034.9304-0.95284.1041-0.064-0.14190.24810.2740.1896-0.403-0.75420.39840.00010.56550.04450.00660.4684-0.03790.337243.676920.583338.4303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 123 )
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 144 )
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 175 )
6X-RAY DIFFRACTION6chain 'A' and (resid 176 through 196 )
7X-RAY DIFFRACTION7chain 'B' and (resid 142 through 177 )
8X-RAY DIFFRACTION8chain 'B' and (resid 178 through 213 )
9X-RAY DIFFRACTION9chain 'B' and (resid 214 through 242 )

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