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- PDB-8cza: Crystal structure of the first bromodomain (BD1) of human BRDT bo... -

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Basic information

Entry
Database: PDB / ID: 8cza
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to GXH-IV-075
ComponentsBromodomain testis-specific protein
KeywordsGENE REGULATION / BRDT / BRD / BET / contraceptive / cancer
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / 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-ZN1 / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsChan, A. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)1U54HD093540 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity.
Authors: Guan, X. / Cheryala, N. / Karim, R.M. / Chan, A. / Berndt, N. / Qi, J. / Georg, G.I. / Schonbrunn, E.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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
E: Bromodomain testis-specific protein
F: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,08711
Polymers79,9166
Non-polymers4,1715
Water724
1
A: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0143
Polymers26,6392
Non-polymers1,3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bromodomain testis-specific protein
D: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0605
Polymers26,6392
Non-polymers1,4213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Bromodomain testis-specific protein
F: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0143
Polymers26,6392
Non-polymers1,3751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.801, 175.737, 143.071
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-202-

NA

21D-201-

NA

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Components

#1: Protein
Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13319.365 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Production host: Escherichia coli (E. coli) / References: UniProt: Q58F21
#2: Chemical ChemComp-ZN1 / 4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluoro-N-[1-(14-{3-[(2-{3-fluoro-4-[(piperidin-4-yl)carbamoyl]anilino}-5-methylpyrimidin-4-yl)amino]-5-[(2-methylpropane-2-sulfonyl)amino]phenyl}-14-oxo-4,7,10-trioxa-13-azatetradecanan-1-oyl)piperidin-4-yl]benzamide


Mass: 1375.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C64H82ClF2N15O11S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / 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: 2.96→47.4 Å / Num. obs: 24746 / % possible obs: 97.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 69.1 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.255 / Net I/σ(I): 8.9
Reflection shellResolution: 2.96→3.04 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1835 / CC1/2: 0.373 / Rrim(I) all: 2.23 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCX

4kcx


Resolution: 2.96→47.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 1158 4.69 %
Rwork0.2042 23507 -
obs0.2072 24665 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.51 Å2 / Biso mean: 72.9 Å2 / Biso min: 19.2 Å2
Refinement stepCycle: final / Resolution: 2.96→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5318 0 533 4 5855
Biso mean--76.9 29.95 -
Num. residues----638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.96-3.10.3331370.309929483085100
3.1-3.260.3741300.287329763106100
3.26-3.460.3551280.26612457258583
3.46-3.730.33251560.240429773133100
3.73-4.110.2741560.199629773133100
4.11-4.70.23981340.167930193153100
4.7-5.920.24251710.178130183189100
5.92-47.40.19881460.1723135328199
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)
1-0.01490.0351-0.05580.9345-2.32195.51540.4834-0.668-1.0218-0.03920.38461.0421-0.5804-0.6602-0.70770.36350.07870.02060.65560.07351.0758-3.518140.3091-9.9682
27.7037-1.08254.91086.64040.94893.64320.021-1.222-0.31460.38790.04920.2268-0.3278-1.1382-0.38080.44650.0002-0.04270.4786-0.00870.34589.040845.07791.627
34.1699-2.92521.48364.5119-0.36013.36930.50040.28660.46750.1473-0.2784-0.332-1.63130.2508-0.21330.9889-0.11950.10750.41370.12460.568319.814457.3552-6.9545
45.9215-0.272-0.51382.12071.95551.60650.31210.48260.63420.1613-0.38930.3754-0.9067-0.10420.0750.56510.0304-0.13820.51950.12640.47487.714447.9275-11.0222
52.95764.86585.4839.00639.68411.99770.46330.50911.96970.02221.4072-3.06810.51491.0901-0.40910.54450.03620.19980.7891-0.00010.706228.215844.8378-4.5599
66.34644.99144.15557.11155.70168.82490.52910.2162-0.61330.91560.28630.34640.7591.8537-0.54820.43410.0568-0.12350.27330.14250.516613.288437.6509-3.8347
75.9152-3.75310.78438.7471-1.6482.07820.52420.2148-0.5784-1.1659-0.2099-0.08060.1870.0438-0.37870.6943-0.0953-0.05230.4788-0.00970.315129.513932.9369.1505
88.6409-5.429-5.49436.38670.04487.3547-0.3063-0.65250.47821.04560.0759-0.8128-0.01221.09550.60680.5563-0.15080.02050.58470.01420.414834.13743.491817.9119
94.9471-2.6311-0.35485.9934-0.70531.8381-0.0248-0.1693-0.243-0.4636-0.0424-0.59760.2030.16370.01530.3681-0.0945-0.02310.46890.02420.501535.391131.286915.2462
107.5432-4.03041.86916.1755-2.44944.01140.1324-0.2007-0.7979-0.46220.40671.49750.2796-0.4708-0.6790.4186-0.1623-0.05760.5471-0.00970.377822.317929.300216.7123
116.98026.37615.70276.07495.66825.51950.0853-1.62941.7955-0.4491-0.7144-0.0312-2.2372-0.41580.70420.71360.01150.0860.382-0.01650.6391-9.393224.365528.7377
126.6704-1.8316-0.63772.55193.49586.0380.2723-0.14530.5342-1.17180.2544-0.0082-0.1070.39-0.44520.59470.04430.02150.43040.07440.3747-5.143711.711420.6479
138.25492.05290.07377.4127-2.71663.1922-0.2233-1.1128-0.78280.03440.15440.56220.8364-1.6542-0.04730.5431-0.256-0.01060.7739-0.00550.5969-12.851-2.721928.5246
148.5766-3.82240.00975.55121.52865.5373-0.268-0.32840.0918-0.3051-0.04060.7314-0.69030.43210.31350.48630.2115-0.01090.871-0.18330.524-16.863816.099829.819
154.5228-0.90723.76386.1062-3.14737.188-0.1321-0.39910.2877-0.47260.2496-0.24680.0534-0.9484-0.13360.4559-0.08270.00890.4949-0.12660.4084-4.89095.755133.3029
162.6192-1.03350.09573.27134.01046.6943-0.12360.07440.2958-0.45190.1306-0.25410.19890.24850.1230.459-0.04310.10510.46690.05010.46421.018313.55928.3211
173.0791-2.7234-3.24732.46232.80933.5233-0.4697-0.43650.6087-0.54620.63710.44450.64431.11060.27190.7057-0.118-0.23720.6656-0.01270.938130.8395-0.760315.9743
187.67520.57213.49064.5812-2.06642.78060.2107-0.9515-0.92160.45770.5917-1.2413-0.5921-0.0418-0.71550.53110.13510.01760.5158-0.19070.619415.73963.34718.7003
193.15732.4334.238.852-1.2718.7152-0.1713-0.6744-0.133-0.04051.00280.1788-0.2993-0.8474-0.79150.3618-0.07310.05150.7173-0.02260.41482.2935-8.173414.1669
208.04221.05334.83624.3380.81673.70520.479-0.7119-0.7908-0.12420.3663-0.50260.86750.0106-1.09430.52880.0114-0.01470.4036-0.03570.525114.1067-9.329111.54
215.82045.6170.30348.9925-4.43726.5352-0.2342-1.3550.3433-0.74581.0337-2.97811.05930.9171-0.30970.42830.17060.06450.6872-0.12841.333128.1894-10.528813.589
223.9582.47143.28444.5339-0.56045.0092-0.2454-0.03480.1850.24870.1716-0.3707-0.3250.08010.00590.6095-0.02260.16850.3359-0.13360.449613.6036-1.93815.8791
239.81350.77393.1363.0001-0.67793.38171.1082-0.53911.8391-0.1352-0.6031-0.2566-1.2529-0.0427-0.18280.8159-0.10320.08120.4767-0.2350.599417.90527.08129.7465
249.3116-3.63735.41214.05260.65579.5076-1.2588-0.29691.1241-1.42341.2684-1.0613-1.5391-0.55120.14790.3471-0.17110.15450.6635-0.05071.120538.249866.521955.305
259.11425.53497.91187.72592.8447.7444-0.75632.0982-0.4474-1.59130.0699-1.1813-0.6141.48661.15130.6203-0.1990.05190.77950.04030.508732.35559.882246.4169
265.8513-1.9207-1.19934.67580.27968.4181-0.49070.6781-0.17140.10950.54970.6601-0.1982-1.37650.04080.6345-0.1233-0.00580.68180.10850.40116.321753.348852.4914
277.52750.5361-1.9366.43181.74956.19860.23780.65831.03331.01020.08580.802-0.7542-1.1697-0.26720.6782-0.0714-0.17360.41170.14570.805327.149466.982556.6636
287.45732.75311.39217.74952.1462.0150.5856-0.63380.65170.781-1.25090.2863-0.3569-0.41840.5580.6946-0.0409-0.03490.47930.00180.300225.579451.443658.4061
296.21773.85092.90038.41632.12618.0447-0.53930.7784-0.09-0.05080.8817-0.6736-0.45210.6643-0.23940.4836-0.10190.00950.6088-0.09480.434934.537751.198952.0409
304.36532.5904-4.3243.80310.84849.6150.18380.78810.53010.4205-0.7476-1.32771.07722.18080.63230.42440.1512-0.08930.9480.16190.609738.585318.997736.8395
314.22392.3416-4.565.8244-2.28325.00270.3034-0.834-1.21070.62370.3247-2.7656-0.38890.9762-0.27990.5755-0.1142-0.03240.9854-0.16370.684436.041630.102541.7489
326.1027-1.74012.8625.30691.26422.94450.1466-0.1728-0.25090.3129-0.06420.2541-0.84120.2882-0.05770.6304-0.18080.04110.77010.02950.275421.039139.049239.9522
338.2882-5.93563.05184.2524-2.68947.0011-0.05550.7119-0.3257-0.92050.4610.4803-0.3218-0.3879-0.55230.467-0.14790.04460.66450.07510.398316.668932.723931.0958
342.8816-5.01311.14948.9436-3.58993.44650.1934-0.3606-0.5514-0.56810.00110.71050.173-0.3965-0.25150.3817-0.1296-0.07180.595-0.02520.459927.284325.879733.7173
355.4947-4.5702-2.21896.48572.71481.17610.11960.56321.5898-0.481-0.97140.6382-1.04870.7740.81770.2286-0.2470.29970.97520.37970.640723.929646.976828.8389
368.7028-7.4031-0.03845.8348-0.66613.5644-0.00520.20710.60880.4219-0.2631-1.1597-0.45890.42870.38660.4333-0.2218-0.00070.63240.01850.434136.339235.967532.5174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 37 )A27 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 54 )A38 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 75 )A55 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 108 )A76 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 113 )A109 - 113
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 132 )A114 - 132
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 65 )B29 - 65
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 75 )B66 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 108 )B76 - 108
10X-RAY DIFFRACTION10chain 'B' and (resid 109 through 135 )B109 - 135
11X-RAY DIFFRACTION11chain 'C' and (resid 30 through 37 )C30 - 37
12X-RAY DIFFRACTION12chain 'C' and (resid 38 through 52 )C38 - 52
13X-RAY DIFFRACTION13chain 'C' and (resid 53 through 75 )C53 - 75
14X-RAY DIFFRACTION14chain 'C' and (resid 76 through 90 )C76 - 90
15X-RAY DIFFRACTION15chain 'C' and (resid 91 through 113 )C91 - 113
16X-RAY DIFFRACTION16chain 'C' and (resid 114 through 135 )C114 - 135
17X-RAY DIFFRACTION17chain 'D' and (resid 30 through 37 )D30 - 37
18X-RAY DIFFRACTION18chain 'D' and (resid 38 through 52 )D38 - 52
19X-RAY DIFFRACTION19chain 'D' and (resid 53 through 65 )D53 - 65
20X-RAY DIFFRACTION20chain 'D' and (resid 66 through 83 )D66 - 83
21X-RAY DIFFRACTION21chain 'D' and (resid 84 through 90 )D84 - 90
22X-RAY DIFFRACTION22chain 'D' and (resid 91 through 113 )D91 - 113
23X-RAY DIFFRACTION23chain 'D' and (resid 114 through 134 )D114 - 134
24X-RAY DIFFRACTION24chain 'E' and (resid 28 through 37 )E28 - 37
25X-RAY DIFFRACTION25chain 'E' and (resid 38 through 45 )E38 - 45
26X-RAY DIFFRACTION26chain 'E' and (resid 46 through 75 )E46 - 75
27X-RAY DIFFRACTION27chain 'E' and (resid 76 through 90 )E76 - 90
28X-RAY DIFFRACTION28chain 'E' and (resid 91 through 113 )E91 - 113
29X-RAY DIFFRACTION29chain 'E' and (resid 114 through 135 )E114 - 135
30X-RAY DIFFRACTION30chain 'F' and (resid 28 through 37 )F28 - 37
31X-RAY DIFFRACTION31chain 'F' and (resid 38 through 45 )F38 - 45
32X-RAY DIFFRACTION32chain 'F' and (resid 46 through 65 )F46 - 65
33X-RAY DIFFRACTION33chain 'F' and (resid 66 through 75 )F66 - 75
34X-RAY DIFFRACTION34chain 'F' and (resid 76 through 108 )F76 - 108
35X-RAY DIFFRACTION35chain 'F' and (resid 109 through 113 )F109 - 113
36X-RAY DIFFRACTION36chain 'F' and (resid 114 through 133 )F114 - 133

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