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- PDB-1taf: DROSOPHILA TBP ASSOCIATED FACTORS DTAFII42/DTAFII62 HETEROTETRAMER -

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Basic information

Entry
Database: PDB / ID: 1taf
TitleDROSOPHILA TBP ASSOCIATED FACTORS DTAFII42/DTAFII62 HETEROTETRAMER
Components
  • TFIID TBP ASSOCIATED FACTOR 42
  • TFIID TBP ASSOCIATED FACTOR 62
KeywordsCOMPLEX (TWO TRANSCRIPTION FACTORS) / TRANSCRIPTION INITIATION / HISTONE FOLD
Function / homology
Function and homology information


Regulation of TP53 Activity through Phosphorylation / 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 Pre-transcription Events / RNA polymerase II transcribes snRNA genes / follicle cell of egg chamber development / Ub-specific processing proteases / SLIK (SAGA-like) complex ...Regulation of TP53 Activity through Phosphorylation / 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 Pre-transcription Events / RNA polymerase II transcribes snRNA genes / follicle cell of egg chamber development / Ub-specific processing proteases / SLIK (SAGA-like) complex / SAGA complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / transcription coactivator binding / transcription by RNA polymerase II / transcription coactivator activity / protein heterodimerization activity / nucleus
Similarity search - Function
: / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Histone, subunit A / Histone, subunit A ...: / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / Transcription initiation factor TFIID subunit 6 / TAF6, C-terminal HEAT repeat domain superfamily / TAF6 C-terminal HEAT repeat domain / TAF6, C-terminal HEAT repeat domain / Histone, subunit A / Histone, subunit A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 6 / Transcription initiation factor TFIID subunit 9
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsXie, X. / Kokubo, T. / Cohen, S.L. / Mirza, U.A. / Hoffmann, A. / Chait, B.T. / Roeder, R.G. / Nakatani, Y. / Burley, S.K.
CitationJournal: Nature / Year: 1996
Title: Structural similarity between TAFs and the heterotetrameric core of the histone octamer.
Authors: Xie, X. / Kokubo, T. / Cohen, S.L. / Mirza, U.A. / Hoffmann, A. / Chait, B.T. / Roeder, R.G. / Nakatani, Y. / Burley, S.K.
History
DepositionJun 1, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TFIID TBP ASSOCIATED FACTOR 42
B: TFIID TBP ASSOCIATED FACTOR 62
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9999
Polymers15,5412
Non-polymers4587
Water2,270126
1
A: TFIID TBP ASSOCIATED FACTOR 42
B: TFIID TBP ASSOCIATED FACTOR 62
hetero molecules

A: TFIID TBP ASSOCIATED FACTOR 42
B: TFIID TBP ASSOCIATED FACTOR 62
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99818
Polymers31,0824
Non-polymers91614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8670 Å2
ΔGint-410 kcal/mol
Surface area15660 Å2
MethodPISA, PQS
2
B: TFIID TBP ASSOCIATED FACTOR 62
hetero molecules

B: TFIID TBP ASSOCIATED FACTOR 62
hetero molecules

A: TFIID TBP ASSOCIATED FACTOR 42
hetero molecules

A: TFIID TBP ASSOCIATED FACTOR 42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,99818
Polymers31,0824
Non-polymers91614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
crystal symmetry operation3_645-y+3/2,x-1/2,z+1/41
crystal symmetry operation5_645-x+3/2,y-1/2,-z+1/41
Buried area3920 Å2
ΔGint-365 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.800, 59.800, 111.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TFIID TBP ASSOCIATED FACTOR 42


Mass: 7904.011 Da / Num. of mol.: 1 / Fragment: RESIDUES 19 - 86 / Mutation: C55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q27272
#2: Protein TFIID TBP ASSOCIATED FACTOR 62


Mass: 7636.887 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 70
Source method: isolated from a genetically manipulated source
Details: DTAFII42/DTAFII62 IS A HETEROTETRAMER / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P49847
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMUTATION OF CYS 55 TO SER IN DTAF42 WAS MADE FOR CRYSTALLIZATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→6 Å / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.198 / Rfactor obs: 0.198
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 7 126 1218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.218

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