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- PDB-5m4s: Transcription factor TFIIA as a single chain protein -

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Basic information

Entry
Database: PDB / ID: 5m4s
TitleTranscription factor TFIIA as a single chain protein
ComponentsTranscription initiation factor IIA subunit 2,Transcription initiation factor IIA subunit 1,Transcription initiation factor IIA subunit 1
KeywordsTRANSCRIPTION / TFIID / TFIIA / single chain
Function / homology
Function and homology information


transcription factor TFIIA complex / RNA polymerase II general transcription initiation factor binding / transcription preinitiation complex / 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 ...transcription factor TFIIA complex / RNA polymerase II general transcription initiation factor binding / transcription preinitiation complex / 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 / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / transcription initiation at RNA polymerase II promoter / cell junction / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein heterodimerization activity / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit
Similarity search - Domain/homology
Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsKandiah, E. / Gupta, K.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Elife / Year: 2017
Title: Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID.
Authors: Gupta, K. / Watson, A.A. / Baptista, T. / Scheer, E. / Chambers, A.L. / Koehler, C. / Zou, J. / Obong-Ebong, I. / Kandiah, E. / Temblador, A. / Round, A. / Forest, E. / Man, P. / Bieniossek, ...Authors: Gupta, K. / Watson, A.A. / Baptista, T. / Scheer, E. / Chambers, A.L. / Koehler, C. / Zou, J. / Obong-Ebong, I. / Kandiah, E. / Temblador, A. / Round, A. / Forest, E. / Man, P. / Bieniossek, C. / Laue, E.D. / Lemke, E.A. / Rappsilber, J. / Robinson, C.V. / Devys, D. / Tora, L. / Berger, I.
History
DepositionOct 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor IIA subunit 2,Transcription initiation factor IIA subunit 1,Transcription initiation factor IIA subunit 1


Theoretical massNumber of molelcules
Total (without water)24,1341
Polymers24,1341
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.312, 123.312, 34.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcription initiation factor IIA subunit 2,Transcription initiation factor IIA subunit 1,Transcription initiation factor IIA subunit 1 / General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIAS / Transcription initiation ...General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIAS / Transcription initiation factor IIA gamma chain / TFIIA-gamma / General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa subunit / TFIIA-42 / General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa subunit / TFIIA-42


Mass: 24134.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2, GTF2A1, TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657, UniProt: P52655
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.16 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20mM Tris (8.0), 1mM DTT, 0.5mM EDTA and 25mM NaCl

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.38→53.4 Å / Num. obs: 12483 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 11.5
Reflection shellResolution: 2.38→2.52 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.72 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→40.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.606 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.225
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 601 4.8 %RANDOM
Rwork0.1836 ---
obs0.1864 11859 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.18 Å2 / Biso mean: 38.444 Å2 / Biso min: 15.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.38→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 0 50 1739
Biso mean---34.16 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221722
X-RAY DIFFRACTIONr_angle_refined_deg2.0881.9432331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7075208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8125.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.815317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1521512
X-RAY DIFFRACTIONr_chiral_restr0.1570.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021300
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 46 -
Rwork0.274 854 -
all-900 -
obs--99.89 %

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