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- PDB-4rgw: Crystal Structure of a TAF1-TAF7 Complex in Human Transcription F... -

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Basic information

Entry
Database: PDB / ID: 4rgw
TitleCrystal Structure of a TAF1-TAF7 Complex in Human Transcription Factor IID
Components
  • Transcription initiation factor TFIID subunit 1
  • Transcription initiation factor TFIID subunit 7
KeywordsTransferase/Transcription / triple barrel / winged helix / transcriptional regulation / DNA binding / Phosphorylation / nucleus / Transferase-Transcription complex
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / positive regulation of androgen receptor activity / TFIIH-class transcription factor complex binding / histone H4K16ac reader activity / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition ...spermine transport / negative regulation of MHC class I biosynthetic process / positive regulation of androgen receptor activity / TFIIH-class transcription factor complex binding / histone H4K16ac reader activity / negative regulation of protein autoubiquitination / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / RNA polymerase II general transcription initiation factor binding / nuclear vitamin D receptor binding / nuclear thyroid hormone receptor binding / cellular response to ATP / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / histone acetyltransferase binding / midbrain development / 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 / histone acetyltransferase activity / ubiquitin conjugating enzyme activity / transcription initiation at RNA polymerase I promoter / P-TEFb complex binding / MLL1 complex / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of transcription initiation by RNA polymerase II / regulation of DNA repair / transcription regulator inhibitor activity / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / estrogen receptor signaling pathway / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / peptidyl-threonine phosphorylation / male germ cell nucleus / regulation of signal transduction by p53 class mediator / negative regulation of protein kinase activity / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / protein polyubiquitination / kinase activity / positive regulation of protein binding / cellular response to UV / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / protein autophosphorylation / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity
Similarity search - Function
TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle ...TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / TAFII55 protein conserved region / TAFII55 protein conserved region / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TATA box-binding protein binding / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID subunit 1, histone acetyltransferase domain / Transcription initiation factor TFIID subunit 1 / Protein of unknown function (DUF3591) / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIID subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsWang, H. / Curran, E.C. / Hinds, T.R. / Wang, E.H. / Zheng, N.
CitationJournal: Cell Res. / Year: 2014
Title: Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module.
Authors: Wang, H. / Curran, E.C. / Hinds, T.R. / Wang, E.H. / Zheng, N.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 1
B: Transcription initiation factor TFIID subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0154
Polymers113,8312
Non-polymers1842
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-37 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.224, 94.542, 101.820
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 TFIID subunit 1 / Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor ...Cell cycle gene 1 protein / TBP-associated factor 250 kDa / p250 / Transcription initiation factor TFIID 250 kDa subunit / TAF(II)250 / TAFII-250 / TAFII250


Mass: 73418.359 Da / Num. of mol.: 1 / Fragment: DUF3591 domain, UNP residues 579-1215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Protein Transcription initiation factor TFIID subunit 7 / RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa ...RNA polymerase II TBP-associated factor subunit F / Transcription initiation factor TFIID 55 kDa subunit / TAF(II)55 / TAFII-55 / TAFII55


Mass: 40412.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF7, TAF2F, TAFII55 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five / References: UniProt: Q15545
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M potassium sodium tartrate tetrahydrate, pH 7.4, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2012
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 36320 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 20.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1776 / % possible all: 96.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.301→47.271 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1813 5 %RANDOM
Rwork0.1856 ---
obs0.188 36253 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→47.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 12 200 4500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084398
X-RAY DIFFRACTIONf_angle_d1.1685921
X-RAY DIFFRACTIONf_dihedral_angle_d15.6561711
X-RAY DIFFRACTIONf_chiral_restr0.078629
X-RAY DIFFRACTIONf_plane_restr0.004760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.36290.24541230.21932572X-RAY DIFFRACTION98
2.3629-2.43240.23761290.20712607X-RAY DIFFRACTION100
2.4324-2.51090.26911410.20672582X-RAY DIFFRACTION100
2.5109-2.60060.25691500.20992630X-RAY DIFFRACTION100
2.6006-2.70470.27351300.20652634X-RAY DIFFRACTION100
2.7047-2.82780.28011460.2052616X-RAY DIFFRACTION100
2.8278-2.97690.26221390.20982639X-RAY DIFFRACTION100
2.9769-3.16340.28311480.21242630X-RAY DIFFRACTION100
3.1634-3.40750.21191500.19122642X-RAY DIFFRACTION100
3.4075-3.75030.23491260.17582679X-RAY DIFFRACTION100
3.7503-4.29270.21631420.16362673X-RAY DIFFRACTION100
4.2927-5.40710.20981430.14662705X-RAY DIFFRACTION100
5.4071-47.2810.19061460.17762831X-RAY DIFFRACTION100

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