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- PDB-7k3o: Crystal structure of the unliganded second bromodomain (BD2) of h... -

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Basic information

Entry
Database: PDB / ID: 7k3o
TitleCrystal structure of the unliganded second bromodomain (BD2) of human TAF1
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / TAF1 / non-BET / BET / kinase inhibitor / ATR / dual BRD-kinase / transferase-transferase inhibitor complex
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 / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...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 / 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 / midbrain development / cellular response to ATP / negative regulation of signal transduction by p53 class mediator / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / 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 / p53 binding / cellular response to UV / 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, conserved site ...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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKarim, M.R. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery of Dual TAF1-ATR Inhibitors and Ligand-Induced Structural Changes of the TAF1 Tandem Bromodomain.
Authors: Karim, R.M. / Yang, L. / Chen, L. / Bikowitz, M.J. / Lu, J. / Grassie, D. / Shultz, Z.P. / Lopchuk, J.M. / Chen, J. / Schonbrunn, E.
History
DepositionSep 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)32,82718
Polymers31,7662
Non-polymers1,06116
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint4 kcal/mol
Surface area13300 Å2
Unit cell
Length a, b, c (Å)57.180, 57.420, 124.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1499 through 1557 or resid 1559...
21(chain B and (resid 1499 through 1557 or resid 1559...

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
11SERSERILEILE(chain A and (resid 1499 through 1557 or resid 1559...AA1499 - 15571 - 59
12LYSLYSGLUGLU(chain A and (resid 1499 through 1557 or resid 1559...AA1559 - 156661 - 68
13PHEPHEILEILE(chain A and (resid 1499 through 1557 or resid 1559...AA1568 - 157570 - 77
14ALAALATHRTHR(chain A and (resid 1499 through 1557 or resid 1559...AA1577 - 160579 - 107
15TYRTYRALAALA(chain A and (resid 1499 through 1557 or resid 1559...AA1607 - 1621109 - 123
21SERSERILEILE(chain B and (resid 1499 through 1557 or resid 1559...BB1499 - 15571 - 59
22LYSLYSGLUGLU(chain B and (resid 1499 through 1557 or resid 1559...BB1559 - 156661 - 68
23PHEPHEILEILE(chain B and (resid 1499 through 1557 or resid 1559...BB1568 - 157570 - 77
24ALAALATHRTHR(chain B and (resid 1499 through 1557 or resid 1559...BB1577 - 160579 - 107
25TYRTYRALAALA(chain B and (resid 1499 through 1557 or resid 1559...BB1607 - 1621109 - 123

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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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 2.0 M Ammonium sulfate, 25% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→38.52 Å / Num. obs: 45208 / % possible obs: 98.7 % / Redundancy: 6.596 % / Biso Wilson estimate: 37.617 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.04 / Χ2: 1.067 / Net I/σ(I): 26.06 / Num. measured all: 298199
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.746.7250.7372.9122218335533040.860.79898.5
1.74-1.796.4970.5843.6520803324932020.910.63598.6
1.79-1.846.1730.4474.8219049318230860.930.48897
1.84-1.97.0580.336721442307330380.9710.36398.9
1.9-1.967.0810.2529.1220923298729550.9850.27298.9
1.96-2.037.0290.18311.8320139289428650.9920.19899
2.03-2.116.9190.13315.5619034278527510.9950.14498.8
2.11-2.196.8480.09920.1318291269826710.9960.10799
2.19-2.296.7020.07225.5517257259725750.9980.07899.2
2.29-2.46.540.0629.6815996247024460.9980.06699
2.4-2.536.040.05530.7814036235623240.9980.06198.6
2.53-2.696.3480.04637.1813814223921760.9990.0597.2
2.69-2.876.870.03745.3214524213021140.9990.0499.2
2.87-3.16.7640.03251.0613150195719440.9990.03499.3
3.1-3.46.4830.02955.5411786182618180.9990.03299.6
3.4-3.86.2710.02461.7410442167216650.9990.02699.6
3.8-4.396.0140.02364.098823147414670.9990.02599.5
4.39-5.385.5680.02262.036838126712280.9990.02496.9
5.38-7.66.3580.02165.586358100110000.9990.02399.9
7.6-38.525.6580.01865.42327659757910.0297

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JJG

7jjg


Resolution: 1.7→38.52 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2023 994 2.2 %
Rwork0.1734 44208 -
obs0.174 45202 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.51 Å2 / Biso mean: 40.6116 Å2 / Biso min: 18.36 Å2
Refinement stepCycle: final / Resolution: 1.7→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2004 0 78 180 2262
Biso mean--50.77 46.26 -
Num. residues----246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A688X-RAY DIFFRACTION0.911TORSIONAL
12B688X-RAY DIFFRACTION0.911TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.790.27051400.22546210635099
1.79-1.90.23041390.20926199633898
1.9-2.050.21481410.18926244638599
2.05-2.250.21111410.1746276641799
2.25-2.580.2091410.17566277641898
2.58-3.250.19761440.18086391653599
3.25-38.520.19151480.166611675999
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)
12.1939-0.4556-0.31964.37920.10762.4260.085-0.0572-0.00130.2207-0.0116-0.2517-0.11780.3776-0.05920.2239-0.0022-0.0360.1921-0.03360.17324.942155.29628.6799
22.13840.421-0.65057.06290.7453.98090.0640.0430.0546-0.2780.0645-0.6217-0.23080.4739-0.12060.18660.00790.00410.271-0.0370.23987.411354.304320.4016
33.8632-1.42880.46477.5268-4.05228.0449-0.08680.0660.020.1882-0.04910.0961-0.2079-0.15310.05860.13420.029-0.01690.1641-0.0390.1571-3.505549.08919.8231
48.81525.27230.71557.0686-1.31427.58170.09110.82111.1336-0.77130.05670.3486-0.62110.3177-0.29130.99090.07590.0530.41430.1050.60812.04471.838314.1842
54.7895-0.029-0.18024.37971.42745.8833-0.0983-0.5129-0.0380.02630.12480.53120.5987-0.8261-0.04290.2194-0.027-0.04130.58440.0160.2647-22.850842.9916.3831
62.1228-1.53582.15466.2009-2.142.2811-0.07980.75970.1991-0.0662-0.1091-0.2964-0.1826-0.04870.21950.2418-0.00250.00220.4027-0.02190.2568-4.49847.05910.2521
76.6065-3.934-1.53017.90523.47955.72890.19810.8571-0.4924-0.1821-0.3959-0.0440.74320.30090.15380.35960.05510.05980.4439-0.10040.36142.664634.0131-0.8342
85.908-1.81591.2551.9076-2.00164.0879-0.04430.2872-0.5462-0.0449-0.00290.10970.6282-0.1341-0.0050.32810.0064-0.00550.2646-0.09670.2968-5.528634.60336.4879
96.07972.53063.72338.953-0.47277.6860.1481-0.6499-0.83960.378-0.21430.54860.8831-1.32570.10310.3138-0.10450.01220.59230.0430.423-19.465136.161611.3479
103.51580.28371.49543.5231-1.33615.1714-0.0972-0.2165-0.28780.1750.06730.11520.1546-0.2807-0.02050.19130.0193-0.02170.1709-0.04580.1729-4.7441.514513.2198
111.603-0.8527-3.46074.37611.5898.41130.09520.08720.2619-0.1495-0.2097-0.0757-0.4840.19410.06420.2375-0.0096-0.0450.2174-0.01360.2208-2.714350.17929.4146
126.14624.3549-2.24446.0783-1.51563.0054-0.107-0.05060.35970.45710.24841.0381-0.068-0.5972-0.35790.53540.16440.02421.2925-0.18740.7657-25.684346.808116.5976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1499 through 1558 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1559 through 1583 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1584 through 1606 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1607 through 1621 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1499 through 1517 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1518 through 1528 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 1529 through 1539 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 1540 through 1558 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1559 through 1564 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1565 through 1582 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1583 through 1606 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1607 through 1621 )B0

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