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- PDB-7ubo: Crystal Structure of the first bromodomain of human BRDT in compl... -

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Basic information

Entry
Database: PDB / ID: 7ubo
TitleCrystal Structure of the first bromodomain of human BRDT in complex with the inhibitor CCD-956
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION/INHIBITOR / INHIBITOR / REGULATOR / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of gene expression / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-MJN / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsTa, H.M. / Modukuri, R.K. / Yu, Z. / Tan, Z. / Matzuk, M.M. / Kim, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)P01HD087157 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Discovery of potent BET bromodomain 1 stereoselective inhibitors using DNA-encoded chemical library selections.
Authors: Modukuri, R.K. / Yu, Z. / Tan, Z. / Ta, H.M. / Ucisik, M.N. / Jin, Z. / Anglin, J.L. / Sharma, K.L. / Nyshadham, P. / Li, F. / Riehle, K. / Faver, J.C. / Duong, K. / Nagarajan, S. / Simmons, ...Authors: Modukuri, R.K. / Yu, Z. / Tan, Z. / Ta, H.M. / Ucisik, M.N. / Jin, Z. / Anglin, J.L. / Sharma, K.L. / Nyshadham, P. / Li, F. / Riehle, K. / Faver, J.C. / Duong, K. / Nagarajan, S. / Simmons, N. / Palmer, S.S. / Teng, M. / Young, D.W. / Yi, J.S. / Kim, C. / Matzuk, M.M.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 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: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
C: Bromodomain testis-specific protein
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9269
Polymers52,5854
Non-polymers2,3415
Water8,593477
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,1461
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7903
Polymers13,1461
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,1461
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,1461
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.691, 94.382, 112.651
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
Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13146.237 Da / Num. of mol.: 4 / Fragment: first bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_Alpha_S (others)
References: UniProt: Q58F21
#2: Chemical
ChemComp-MJN / N-[(2R)-1-(methylamino)-3-{1-[(4-methyl-2-oxo-1,2-dihydroquinolin-6-yl)acetyl]piperidin-4-yl}-1-oxopropan-2-yl]-5-phenylpyridine-2-carboxamide


Mass: 565.662 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H35N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.26 M Ammonium Sulfate, 0.1 M Tris 8.5, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→48.37 Å / Num. obs: 113916 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 8.3
Reflection shellResolution: 1.82→1.885 Å / Num. unique obs: 5882 / CC1/2: 0.306 / CC star: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FLP

4flp


Resolution: 1.82→48.37 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 3820 3.35 %
Rwork0.1772 110096 -
obs0.1779 113916 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.28 Å2 / Biso mean: 34.0164 Å2 / Biso min: 16.29 Å2
Refinement stepCycle: final / Resolution: 1.82→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 178 477 4209
Biso mean--30.97 41.15 -
Num. residues----434
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-1.840.3721390.348440264165
1.84-1.870.31081460.333441384284
1.87-1.890.32591390.306840204159
1.89-1.920.32091460.302241714317
1.92-1.950.29951400.27839954135
1.95-1.980.27531460.263841334279
1.98-2.010.24451440.243540564200
2.01-2.050.25761410.228940794220
2.05-2.080.23971420.218740664208
2.08-2.120.20921440.193240954239
2.12-2.170.23221410.190140554196
2.17-2.210.23951450.188341104255
2.21-2.270.19961430.1940534196
2.27-2.320.22661420.186240384180
2.32-2.380.19951360.180341104246
2.38-2.450.21761400.174540904230
2.46-2.530.22151380.164740584196
2.53-2.620.1861420.172541314273
2.62-2.730.21851370.168740244161
2.73-2.850.18291450.176540904235
2.85-30.21691440.170940914235
3-3.190.23411420.172940804222
3.19-3.440.18121350.157840834218
3.44-3.780.14631410.14340804221
3.79-4.330.15421390.131240814220
4.33-5.460.15361470.142640664213
5.46-48.370.16941360.165640774213
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)
19.00965.12834.98893.47434.3487.85540.22220.2405-0.78090.13180.1271-0.68810.47740.545-0.32570.21370.03410.00780.24960.0260.258212.64-32.78412.085
26.9633-6.7304-5.69299.36127.13315.6887-0.039-0.07930.4914-0.07270.4252-0.4965-0.24630.758-0.31470.2175-0.0195-0.00540.24710.02760.19389.152-24.62119.718
37.14224.2117-3.55635.7977-3.03613.67850.1312-0.51740.03180.537-0.13740.2212-0.17960.09760.03650.24270.02040.02830.192-0.00820.1612-4.066-26.2830.497
46.26390.2005-5.69955.4352-1.87228.9804-0.06640.1831-0.4073-0.0099-0.00110.31560.0745-0.35590.16460.2066-0.00830.01860.17760.02280.2753-8.738-35.92225.369
53.9368-1.0218-5.86745.32463.03479.1866-0.4032-0.5449-0.790.6897-0.0062-0.11420.55630.60940.3050.22530.0190.02250.21110.09710.3027.203-35.41723.2
62.6565-2.66951.70976.1364-4.94584.14190.2420.6322-0.7856-0.5681-0.4617-0.18370.2490.41530.12320.33360.07150.0310.216-0.01130.29418.031-41.80416.413
73.7292-0.9365-4.03920.26221.04964.5345-0.19280.1533-0.5846-0.03930.04460.36520.2143-0.09240.19950.1954-0.0073-0.00470.14370.00590.2686-4.151-31.87517.181
86.05644.86296.00124.83675.42456.3402-0.157-0.92260.55680.2732-0.1052.6259-0.5512-0.66710.36550.2640.03060.01590.2831-0.00340.4911-14.701-21.16823.973
95.1975-3.8502-5.48462.75714.07215.1420.0980.41540.1391-0.0669-0.1746-0.0265-0.1382-0.3469-0.04570.2401-0.0007-0.01280.23620.00830.26150.86-22.98813.413
103.4636-0.0737-1.0932.57090.82767.1314-0.1126-1.4191-0.28681.1240.0967-0.9940.57820.6610.02410.39150.0717-0.1320.3426-0.00490.320418.284-8.76637.178
113.3158-4.3391.46125.8565-2.56482.9659-0.5445-0.58750.51650.62650.3273-0.1808-0.20420.0980.17520.32910.01410.02270.2426-0.05590.21649.332-1.4135.451
124.40941.74521.96936.31392.10133.87090.1893-0.09450.116-0.067-0.25090.5676-0.0249-0.39020.07380.19210.03550.03310.1974-0.00510.2527-3.152-3.49824.117
135.7971-1.08815.04414.8339-2.4696.7840.1351-0.1123-0.22070.1756-0.0599-0.04090.45250.053-0.15490.22550.01110.03990.152-0.00380.16666.737-13.35926.471
147.6157-2.27226.05631.2113-2.08785.02840.20690.0286-0.036-0.0688-0.0351-0.06130.21370.1982-0.18410.26570.0210.02960.1991-0.03570.20510.575-6.97321.4
154.4738-1.65320.25532.57021.48932.11620.55080.65930.8584-1.7122-0.34380.3743-0.7304-0.345-0.04330.41890.05980.04290.26510.03720.35161.0283.64613.205
163.7211-2.40474.38064.2938-1.5826.89090.025-0.23570.3570.20830.0673-0.4938-0.10180.4414-0.00510.21840.00430.03210.2093-0.05990.240913.7011.89426.796
173.263-1.38680.46214.7943-2.12724.153-0.04990.4040.034-0.30260.13490.0926-0.0776-0.1419-0.10610.1562-0.0517-0.00350.2696-0.01660.134816.238-17.357-2.876
185.5286-2.83920.78443.835-0.50191.2737-0.0412-0.02770.030.06450.17780.1151-0.1495-0.0545-0.12290.2091-0.03320.03560.2470.02030.149413.779-14.9155.363
195.5357-3.4786-1.27495.7850.66341.5550.1071-0.02760.3284-0.37070.0707-0.2996-0.18470.1058-0.14380.2292-0.05120.03710.3131-0.02090.170924.686-12.086-1.539
207.13641.31813.19445.49773.17312.791-0.16240.3740.6373-0.62640.18030.1776-1.4781-0.14280.05820.4311-0.00120.08060.24070.02180.403922.4859.0176.191
214.0498-0.7792-0.00731.8159-2.45773.92990.1112-0.09960.35450.2079-0.0363-0.65740.11170.8318-0.08440.2675-0.0304-0.05280.4208-0.19240.452334.292-2.83519.346
226.6922-3.586-1.25393.4616-1.0773.5622-0.07120.05870.6191-0.35320.3202-1.8075-0.02830.8447-0.1280.2931-0.06140.070.4685-0.13030.609938.974-6.7099.634
235.26032.380.94388.3254-5.4865.09350.07490.6080.7846-0.89190.2864-0.3722-0.50920.8622-0.1790.5075-0.16160.20130.41860.01050.646532.8528.1043.683
245.1874-3.9843.82925.8696-2.71846.01540.1370.21350.5228-0.482-0.1227-0.5161-0.14590.59190.06980.2637-0.07930.09230.3222-0.06650.360329.351-4.3546.166
258.6352-5.5536-6.55124.52214.49875.0653-0.87510.1845-0.71240.59720.11830.04841.6028-0.26740.67120.3497-0.00520.06510.3242-0.05620.358328.856-14.53918.802
268.4658-5.79896.78929.1959-5.92767.87120.13140.24570.2275-0.2943-0.04750.0201-0.18860.1256-0.13370.191-0.01360.06310.2408-0.05030.250219.395-1.7589.486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:37 )A29 - 37
2X-RAY DIFFRACTION2( CHAIN A AND RESID 38:45 )A38 - 45
3X-RAY DIFFRACTION3( CHAIN A AND RESID 46:65 )A46 - 65
4X-RAY DIFFRACTION4( CHAIN A AND RESID 66:75 )A66 - 75
5X-RAY DIFFRACTION5( CHAIN A AND RESID 76:84 )A76 - 84
6X-RAY DIFFRACTION6( CHAIN A AND RESID 85:90 )A85 - 90
7X-RAY DIFFRACTION7( CHAIN A AND RESID 91:108 )A91 - 108
8X-RAY DIFFRACTION8( CHAIN A AND RESID 109:113 )A109 - 113
9X-RAY DIFFRACTION9( CHAIN A AND RESID 114:136 )A114 - 136
10X-RAY DIFFRACTION10( CHAIN B AND RESID 29:37 )B29 - 37
11X-RAY DIFFRACTION11( CHAIN B AND RESID 38:45 )B38 - 45
12X-RAY DIFFRACTION12( CHAIN B AND RESID 46:65 )B46 - 65
13X-RAY DIFFRACTION13( CHAIN B AND RESID 66:90 )B66 - 90
14X-RAY DIFFRACTION14( CHAIN B AND RESID 91:108 )B91 - 108
15X-RAY DIFFRACTION15( CHAIN B AND RESID 109:113 )B109 - 113
16X-RAY DIFFRACTION16( CHAIN B AND RESID 114:136 )B114 - 136
17X-RAY DIFFRACTION17( CHAIN C AND RESID 28:65 )C28 - 65
18X-RAY DIFFRACTION18( CHAIN C AND RESID 66:108 )C66 - 108
19X-RAY DIFFRACTION19( CHAIN C AND RESID 109:135 )C109 - 135
20X-RAY DIFFRACTION20( CHAIN D AND RESID 29:45 )D29 - 45
21X-RAY DIFFRACTION21( CHAIN D AND RESID 46:65 )D46 - 65
22X-RAY DIFFRACTION22( CHAIN D AND RESID 66:75 )D66 - 75
23X-RAY DIFFRACTION23( CHAIN D AND RESID 76:90 )D76 - 90
24X-RAY DIFFRACTION24( CHAIN D AND RESID 91:108 )D91 - 108
25X-RAY DIFFRACTION25( CHAIN D AND RESID 109:113 )D109 - 113
26X-RAY DIFFRACTION26( CHAIN D AND RESID 114:136 )D114 - 136

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