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- PDB-7t36: Crystal structure of the tandem bromodomain (BD1 and BD2) of huma... -

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Basic information

Entry
Database: PDB / ID: 7t36
TitleCrystal structure of the tandem bromodomain (BD1 and BD2) of human TAF1 bound to ZS1-322
ComponentsTranscription initiation factor TFIID subunit 1
KeywordsGENE REGULATION / TAF1 / TATA binding protein / transcription / PIC / TBP associated factor 1 / Bromodomains
Function / homology
Function and homology information


negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / midbrain development / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape ...negative regulation of protein autoubiquitination / regulation of cell cycle G1/S phase transition / RNA polymerase I general transcription initiation factor activity / positive regulation of androgen receptor activity / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor binding / cellular response to ATP / 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 / transcription initiation at RNA polymerase I promoter / ubiquitin conjugating enzyme activity / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / negative regulation of ubiquitin-dependent protein catabolic process / regulation of signal transduction by p53 class mediator / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / peptidyl-threonine phosphorylation / lysine-acetylated histone binding / mRNA transcription by RNA polymerase II / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of protein binding / kinase activity / ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / protein heterodimerization activity / negative regulation of gene expression / protein phosphorylation / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-EIO / Transcription initiation factor TFIID subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKarim, M.R. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS) United States
CitationJournal: To Be Published
Title: Crystal structure of the tandem bromodomain (BD1 and BD2) of human TAF1 bound to ZS1-322
Authors: Karim, M.R. / Schonbrunn, E.
History
DepositionDec 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4975
Polymers30,9681
Non-polymers5294
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.300, 54.299, 122.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / TAFII250


Mass: 30968.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF1, BA2R, CCG1, CCGS, TAF2A / Plasmid: pNIC28.Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: P21675, histone acetyltransferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EIO / (3R)-4-[6-{1-[diamino(hydroxy)-lambda~4~-sulfanyl]cyclopropyl}-2-(methylsulfanyl)pyrimidin-4-yl]-3-methylmorpholine


Mass: 342.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N5O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M MgCl2, 0.1 M Bis-Tris pH 5.5, 15% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→45.3 Å / Num. obs: 37091 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 15.7 / Num. measured all: 237130 / Scaling rejects: 497
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.686.71.0351198017880.7340.4271.1212.998.1
9.04-45.35.30.03414832800.9990.0150.03835.699.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19_4085refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JSP

7jsp


Resolution: 1.65→42.5 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2027 1852 5 %
Rwork0.18 35176 -
obs0.1811 37028 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.19 Å2 / Biso mean: 30.1843 Å2 / Biso min: 13.47 Å2
Refinement stepCycle: final / Resolution: 1.65→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 34 204 2268
Biso mean--29.02 36.11 -
Num. residues----249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.690.27211390.25382627276699
1.69-1.740.26361400.24322672281299
1.74-1.80.25071400.243126552795100
1.8-1.870.2311400.23352672281299
1.87-1.940.25151400.20492655279599
1.94-2.030.19121430.18812704284799
2.03-2.130.19551390.17882661280099
2.14-2.270.21371430.1812714285799
2.27-2.440.22791420.183727012843100
2.44-2.690.21341430.188527142857100
2.69-3.080.22571450.18332736288199
3.08-3.880.17361440.16482758290299
3.88-42.50.17421540.154729073061100
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)
19.30583.598-7.14715.1485-3.22857.69720.3022-0.06730.64240.57880.08870.3363-0.3833-0.1647-0.42830.28090.00820.01140.2412-0.0690.2033-131.0245-147.1821143.5505
22.95240.7276-0.17412.5071-0.05883.9519-0.01680.0140.21360.05050.0560.0536-0.1915-0.2788-0.06510.12190.0221-0.00170.12940.00960.175-129.3345-147.9223126.6786
35.0796-0.7442-3.88822.38881.7086.1429-0.2615-0.1743-0.0910.30390.0846-0.05970.5895-0.06360.31270.1550.0029-0.00350.1065-0.00870.1376-124.6869-156.6699128.6507
46.61161.2162-5.21724.2923-2.28815.9047-0.0048-0.66530.03140.47720.0718-0.1154-0.06680.3109-0.02410.1602-0.0002-0.04470.2058-0.01090.1487-118.6343-153.6337136.1455
58.18473.62971.36073.58611.78433.90480.342-0.6912-0.35340.7894-0.248-0.10850.4973-0.009-0.06410.4684-0.05710.02960.38370.00790.1642-135.0138-159.8719150.2033
68.7883-3.6934-5.46778.38715.50324.8406-0.1096-0.5431-0.13870.95750.1739-0.30370.43490.5691-0.10620.2758-0.0475-0.07520.24470.07820.1904-135.8795-176.523141.4391
72.50962.0097-1.95677.1294-2.48024.3185-0.0331-0.1251-0.0643-0.144-0.1105-0.1188-0.12160.08930.14650.1168-0.0075-0.0230.1704-0.04580.1672-132.1586-170.4084120.0486
81.88240.2288-1.75411.36250.64992.26970.0915-0.1612-0.0560.1418-0.10340.0187-0.1566-0.02930.00320.1595-0.0191-0.01790.166-0.0110.1877-139.7743-171.7243129.205
95.14252.9889-4.22223.9693-3.46813.867-0.09150.0059-0.5725-0.0214-0.073-0.25080.38940.15360.22730.19380.0054-0.00980.1328-0.03160.3215-138.7097-183.2661123.2589
103.4369-4.2883-3.59815.60345.49656.7635-0.0277-0.20290.09190.5471-0.01030.09570.3734-0.5520.13140.3767-0.10910.01760.40640.02520.2429-147.819-174.6152147.1502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1379 through 1397 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1398 through 1441 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1442 through 1464 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1465 through 1483 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1484 through 1501 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1502 through 1517 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1518 through 1549 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1550 through 1583 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1584 through 1606 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1607 through 1627 )A0

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