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- PDB-7l9a: Crystal structure of BRDT bromodomain 2 in complex with CDD-1102 -

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Basic information

Entry
Database: PDB / ID: 7l9a
TitleCrystal structure of BRDT bromodomain 2 in complex with CDD-1102
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION/INHIBITOR / TRANSCRIPTION-INHIBITOR complex
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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-XWP / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsSharma, R. / Kaur, G. / Yu, Z. / Ku, A.F. / Anglin, J.L. / Ucisik, M.N. / Faver, J.C. / Sankaran, B. / Kim, C. / Matzuk, M.M.
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: 2021
Title: Discovery and characterization of bromodomain 2-specific inhibitors of BRDT.
Authors: Yu, Z. / Ku, A.F. / Anglin, J.L. / Sharma, R. / Ucisik, M.N. / Faver, J.C. / Li, F. / Nyshadham, P. / Simmons, N. / Sharma, K.L. / Nagarajan, S. / Riehle, K. / Kaur, G. / Sankaran, B. / ...Authors: Yu, Z. / Ku, A.F. / Anglin, J.L. / Sharma, R. / Ucisik, M.N. / Faver, J.C. / Li, F. / Nyshadham, P. / Simmons, N. / Sharma, K.L. / Nagarajan, S. / Riehle, K. / Kaur, G. / Sankaran, B. / Storl-Desmond, M. / Palmer, S.S. / Young, D.W. / Kim, C. / Matzuk, M.M.
History
DepositionJan 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8026
Polymers31,5522
Non-polymers1,2504
Water70339
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4013
Polymers15,7761
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4013
Polymers15,7761
Non-polymers6252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.470, 56.470, 191.901
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11ALAALAVALVAL(chain 'A' and (resid 266 through 269 or resid 271...AA266 - 26822 - 24
12GLNGLNGLNGLN(chain 'A' and (resid 266 through 269 or resid 271...AA27127
13HISHISLEULEU(chain 'A' and (resid 266 through 269 or resid 271...AA274 - 28330 - 39
14HISHISVALVAL(chain 'A' and (resid 266 through 269 or resid 271...AA287 - 29843 - 54
15ALAALAVALVAL(chain 'A' and (resid 266 through 269 or resid 271...AA302 - 31158 - 67
16ASNASNTHRTHR(chain 'A' and (resid 266 through 269 or resid 271...AA314 - 32070 - 76
17GLUGLUMETMET(chain 'A' and (resid 266 through 269 or resid 271...AA323 - 32579 - 81
18GLNGLNALAALA(chain 'A' and (resid 266 through 269 or resid 271...AA328 - 33384 - 89
19PHEPHECYSCYS(chain 'A' and (resid 266 through 269 or resid 271...AA336 - 34792 - 103
110TYRTYRILEILE(chain 'A' and (resid 266 through 269 or resid 271...AA350 - 377106 - 133
21ALAALAVALVAL(chain 'B' and (resid 266 through 269 or resid 271...BB266 - 26822 - 24
22GLNGLNGLNGLN(chain 'B' and (resid 266 through 269 or resid 271...BB27127
23HISHISLEULEU(chain 'B' and (resid 266 through 269 or resid 271...BB274 - 28330 - 39
24HISHISVALVAL(chain 'B' and (resid 266 through 269 or resid 271...BB287 - 29843 - 54
25ALAALAVALVAL(chain 'B' and (resid 266 through 269 or resid 271...BB302 - 31158 - 67
26ASNASNTHRTHR(chain 'B' and (resid 266 through 269 or resid 271...BB314 - 32070 - 76
27GLUGLUMETMET(chain 'B' and (resid 266 through 269 or resid 271...BB323 - 32579 - 81
28GLNGLNALAALA(chain 'B' and (resid 266 through 269 or resid 271...BB328 - 33384 - 89
29PHEPHECYSCYS(chain 'B' and (resid 266 through 269 or resid 271...BB336 - 34792 - 103
210TYRTYRILEILE(chain 'B' and (resid 266 through 269 or resid 271...BB350 - 377106 - 133

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Components

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


Mass: 15776.041 Da / Num. of mol.: 2 / Fragment: bromodomain 2
Source method: isolated from a genetically manipulated source
Details: CDD / Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q58F21
#2: Chemical ChemComp-XWP / N~1~-(5-{[3-(4-amino-2-methylphenyl)-1-methyl-1H-indazole-5-carbonyl]amino}-2-methylphenyl)-N~4~-methylbenzene-1,4-dicarboxamide


Mass: 546.619 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H30N6O3 / Details: BRDt BD2 inhibitor / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 0.8 M succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→48.9 Å / Num. obs: 17166 / % possible obs: 99.61 % / Redundancy: 2 % / Biso Wilson estimate: 44.34 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.4
Reflection shellResolution: 2.27→2.35 Å / Num. unique obs: 1680 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uyg

4uyg


Resolution: 2.27→48.9 Å / SU ML: 0.2875 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2654 888 5.17 %
Rwork0.235 16278 -
obs0.2365 17166 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.21 Å2
Refinement stepCycle: LAST / Resolution: 2.27→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 90 39 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552011
X-RAY DIFFRACTIONf_angle_d0.82732735
X-RAY DIFFRACTIONf_chiral_restr0.0463276
X-RAY DIFFRACTIONf_plane_restr0.0052351
X-RAY DIFFRACTIONf_dihedral_angle_d10.3575265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.410.32261620.32132607X-RAY DIFFRACTION99.57
2.41-2.60.3131570.28072654X-RAY DIFFRACTION99.79
2.6-2.860.32121520.27712655X-RAY DIFFRACTION99.68
2.86-3.270.29151360.25142713X-RAY DIFFRACTION99.82
3.27-4.120.24331300.20682747X-RAY DIFFRACTION99.72
4.12-48.90.23481510.2172902X-RAY DIFFRACTION99.9
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)
14.401085644555.347769674723.645170840368.906480282974.974346432918.79157681439-0.5664906727310.6012458349710.115944601969-0.7433564403360.3790015321380.222864110861-0.2814391141830.2958517604970.2075490038670.414519020018-0.121639517029-0.01464065220030.6534262401160.05523373459480.37658700791917.8253536699-11.3479040556-36.1276650631
21.770554014751.819114898590.722322784561.959759683120.7562198702537.60439562894-0.1094471567440.3386518784370.0738361436155-0.120398979668-0.130551862346-0.0734032392242-0.8159709629531.29469556590.2945791072790.499334300163-0.248041835104-0.04137398787320.4581480198250.02435948788870.37547826945332.2961306488-1.05593456247-18.5940613598
34.1224205053-0.2499314499051.824273153312.20734680741-1.186675750193.38054191152-0.3070825459610.468156755607-0.287466758862-0.07734630198280.39411174607-0.3784849175780.0643049200430.7825001056210.1984607935620.388569993888-0.0408332357246-0.01035136120640.521075823035-0.07735838611710.47978863354131.6418043236-12.6661243309-21.4806281622
45.385467417-0.595846285201-0.5262212646340.77318178515-1.759118665335.1266508271-0.007849833636440.408089964379-0.272645939818-0.07641772932950.22128340401-0.103971184964-0.112233309205-0.0133151975442-0.08405245255820.268247215893-0.0692603960692-0.0286665679070.236508419550.02243891788540.27607826881324.0733551106-11.3573946914-20.0076145903
56.924612497611.563604985623.789403217375.588351021573.539931389483.72462788424-0.313307227256-0.1066721556610.6337021530050.239112713493-0.1824025333430.164128940521-0.503297567393-0.6592451908840.6473517487970.407806955974-0.071311418888-0.06166267667890.2936020558880.01742649001930.33677670103118.1851592869-2.53561599676-20.063649179
64.700065396574.919901808485.274691281886.320669362635.778084031715.98939527682-1.149149132321.99475215816-0.273387881763-0.8982807174311.52915201712-0.00936426372044-0.295298480139-0.512593103289-0.208418660820.41686952978-0.313937012658-0.1151095356420.6741755035550.02518382174330.5712898760818.86136565093-13.3160316614-35.9124774017
72.451635176331.199390448993.677348848265.689346476263.34834565027.864991078020.2484950119860.169267665857-0.8782944355770.05349417745660.298743195830.679376129360.990271704303-1.13124189046-0.4401580085480.79504732296-0.235547138483-0.06431984780530.7480138774240.1334921487050.645389866664-5.83281792016-32.1184571067-13.2859829018
80.8460803375781.71972387190.9779118167563.780953878451.880603291381.22022744979-0.131903300389-0.153290962853-0.374078285685-0.2984884031840.162834553140.1631667977870.631615773211-0.0760752404685-0.04082544508270.618368543993-0.1437709614570.05365556094540.3173688058550.07614301268930.3900667619419.31685644451-29.6041053789-2.50977724294
97.522409107821.98231126031-0.5468931927795.54991209495-1.680156797535.648058429050.324849082552-0.136031894660.6917416204680.292812914749-0.367500027939-0.117356250039-0.227391043242-0.007392463635980.1273159770140.383668291958-0.0040795116648-0.04437626370090.3179664790240.02480088099520.4462780258669.30841039825-12.0866359328-5.00134155367
106.66491389945-1.089530823680.5128290341548.82657642974-5.179172741224.271143926610.00637535057412-0.535318054673-0.2888062377690.347689856653-0.02873687061110.154945638006-0.160580003481-1.5838239293-0.140828060870.557855825351-0.0694121232843-0.08577757617670.6466823596560.03656119051770.437040351404-4.43615148921-22.1946890499-6.40676577648
113.717792961061.94075944233-0.05059808569271.51337558084-0.2505295750372.48006916144-0.07112573896160.0801980901634-0.0480174185885-0.3112002936020.1884721230870.1623300315510.34109221018-0.514889214095-0.1057846480360.490326193144-0.0314903459051-0.09497780013670.4174429876020.09518867751480.3399219103675.2829074147-20.2819253988-13.7550665506
122.3946557511-2.31750460991-1.02622637812.61141872756-0.3564941848763.95014320381-0.1828985658781.07596754135-0.298711761239-0.7328613114710.344401461330.05193563384741.02583215730.16220296665-0.2488329894230.749947454932-0.0991797655693-0.05648340981720.3728489812640.04259705273190.3402879764587.58470669545-29.8171089013-14.938836709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 262 through 282 )
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 326 )
4X-RAY DIFFRACTION4chain 'A' and (resid 327 through 355 )
5X-RAY DIFFRACTION5chain 'A' and (resid 356 through 374 )
6X-RAY DIFFRACTION6chain 'A' and (resid 375 through 379 )
7X-RAY DIFFRACTION7chain 'B' and (resid 265 through 282 )
8X-RAY DIFFRACTION8chain 'B' and (resid 283 through 294 )
9X-RAY DIFFRACTION9chain 'B' and (resid 295 through 317 )
10X-RAY DIFFRACTION10chain 'B' and (resid 318 through 326 )
11X-RAY DIFFRACTION11chain 'B' and (resid 327 through 355 )
12X-RAY DIFFRACTION12chain 'B' and (resid 356 through 378 )

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