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- PDB-6p3a: Crystal Structure Analysis of TAF1 Bromodomain -

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Basic information

Entry
Database: PDB / ID: 6p3a
TitleCrystal Structure Analysis of TAF1 Bromodomain
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsTRANSFERASE / kinase / bromodomain / inhibitor / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of androgen receptor signaling pathway / negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / histone H4K16ac reader activity / RNA polymerase II general transcription initiation factor binding / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / midbrain development / HIV Transcription Initiation ...positive regulation of androgen receptor signaling pathway / negative regulation of protein autoubiquitination / RNA polymerase I general transcription initiation factor activity / regulation of cell cycle G1/S phase transition / histone H4K16ac reader activity / RNA polymerase II general transcription initiation factor binding / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / 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 / cellular response to ATP / negative regulation of signal transduction by p53 class mediator / ubiquitin conjugating enzyme activity / transcription initiation at RNA polymerase I promoter / MLL1 complex / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase activity / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / transcription regulator inhibitor activity / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / p53 binding / kinase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein autophosphorylation / ubiquitin-dependent protein catabolic process / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / non-specific serine/threonine protein kinase / protein kinase activity / protein stabilization / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus
Similarity search - Function
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-like ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-NQP / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of TAF1 Bromodomain
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8914
Polymers31,7662
Non-polymers1,1252
Water362
1
A: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4462
Polymers15,8831
Non-polymers5631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription initiation factor TFIID subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4462
Polymers15,8831
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.430, 92.430, 117.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1522 through 1546 or resid 1548...
21(chain B and (resid 1522 through 1546 or resid 1548...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSER(chain A and (resid 1522 through 1546 or resid 1548...AA1522 - 15463 - 27
12PROPROASNASN(chain A and (resid 1522 through 1546 or resid 1548...AA1548 - 155429 - 35
13LYSLYSLYSLYS(chain A and (resid 1522 through 1546 or resid 1548...AA1555 - 155636 - 37
14METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
15METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
16METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
17METMETNQPNQP(chain A and (resid 1522 through 1546 or resid 1548...AA - C1521 - 40002
21ASPASPSERSER(chain B and (resid 1522 through 1546 or resid 1548...BB1522 - 15463 - 27
22PROPROTYRTYR(chain B and (resid 1522 through 1546 or resid 1548...BB1548 - 156229 - 43
23VALVALVALVAL(chain B and (resid 1522 through 1546 or resid 1548...BB1564 - 160145 - 82
24TYRTYRSERSER(chain B and (resid 1522 through 1546 or resid 1548...BB1603 - 160884 - 89
25TYRTYRGLUGLU(chain B and (resid 1522 through 1546 or resid 1548...BB1610 - 163691 - 117
26ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
27ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
28ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
29ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
210ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003
211ASPASPNQPNQP(chain B and (resid 1522 through 1546 or resid 1548...BB - D1522 - 40003

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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 / TAFII250


Mass: 15882.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Production host: Escherichia coli (E. coli)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-NQP / 4-{[(3R)-1-(but-3-en-1-yl)-3-methyl-4-(oxan-4-yl)-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 562.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H42N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.99→58.72 Å / Num. obs: 10768 / % possible obs: 99.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 87.985 Å2 / Rpim(I) all: 0.07 / Rrim(I) all: 0.242 / Net I/σ(I): 9.1 / Num. measured all: 133276
Reflection shellResolution: 2.99→3.04 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 0.9 / Num. measured all: 7079 / Num. unique obs: 518 / Rpim(I) all: 0.868 / Rrim(I) all: 3.236 / % possible all: 98.3

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UV5

3uv5


Resolution: 2.99→57.108 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.71
RfactorNum. reflection% reflection
Rfree0.2862 532 4.97 %
Rwork0.2548 --
obs0.2564 10713 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.89 Å2 / Biso mean: 103.9829 Å2 / Biso min: 59.94 Å2
Refinement stepCycle: final / Resolution: 2.99→57.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 82 2 2124
Biso mean--114.89 69.4 -
Num. residues----254
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A784X-RAY DIFFRACTION4.904TORSIONAL
12B784X-RAY DIFFRACTION4.904TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9902-3.29110.4551360.385124602596
3.2911-3.76730.37441140.338225112625
3.7673-4.7460.32351290.252225332662
4.746-57.11890.22561530.209326772830
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)
16.29030.2755-0.15922.78571.28015.2867-0.3203-1.135-0.97121.21680.0415-0.6074-1.1492-0.0845-0.05821.28890.1294-0.04921.15490.0380.8827-40.5763-17.736622.1945
24.15542.5444-1.50164.4182-0.09283.92660.33690.06511.4422-0.44930.0772-0.0243-1.68650.2541-0.20281.1670.1931-0.03241.3143-0.02120.6559-43.9294-7.53375.5802
34.99910.4977-1.75490.5578-0.1740.72440.36050.82920.9160.39640.2780.2555-1.2539-1.24-0.22161.2246-0.0276-0.04171.49380.09330.7663-58.4771-12.4430.7271
47.4845-1.4601-0.8074.5003-3.46454.3760.771-0.5014-0.626-1.08990.3129-0.84790.4002-2.2981-0.27071.25380.02270.0371.35690.15811.0727-54.6599-21.19290.6264
53.10420.94351.58722.5096-0.5492.8062-0.4002-0.1174-0.37070.12050.47140.27291.2481-0.8113-0.12861.0528-0.0492-0.0361.0970.03410.8021-45.756-21.03099.051
64.5652-0.5049-0.71422.9314-3.26785.2371-0.9328-0.00190.4866-0.43740.2467-1.039-0.8520.41290.05260.9684-0.14170.06950.8563-0.05850.7071-37.8677-13.82861.7763
75.64451.6593-1.64736.5268-2.69096.4137-0.0971-0.1406-1.85331.3538-0.6598-0.71880.96530.01940.13631.54560.12720.04151.3545-0.10591.0811-34.5867-28.84323.6342
84.7828-0.5434-0.06173.4633-1.59664.414-0.0219-0.60210.71620.1615-0.4691-0.05440.0449-1.1085-0.16331.0935-0.14120.21071.0746-0.02470.8282-32.60513.87592.6186
93.4247-0.0596-0.01176.28261.32922.40460.4975-0.46730.2463-0.95020.6271-0.2105-0.2799-1.0338-0.1161.047-0.159-0.02951.2998-0.27950.9306-33.9624-11.8196-12.2486
103.12751.94740.64174.13721.90514.2623-0.27960.67630.0244-0.19740.2802-0.1043-0.40210.5797-0.08051.3759-0.05990.05511.44650.01830.837-28.09992.1534-7.848
114.54711.36820.47023.7791-0.7274.37580.2758-0.03720.72140.192-1.0213-0.54221.54220.69260.1371.7645-0.15760.02861.3349-0.09641.1009-16.982411.72149.7092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1521 through 1538 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1539 through 1549 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1550 through 1560 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1561 through 1570 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1571 through 1604 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1605 through 1627 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1628 through 1648 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1522 through 1549 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1550 through 1560 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1561 through 1627 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1628 through 1647 )B0

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