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- PDB-7s3p: BD2 domain of human BRD3 bound to Physachenolide C -

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Basic information

Entry
Database: PDB / ID: 7s3p
TitleBD2 domain of human BRD3 bound to Physachenolide C
ComponentsBromodomain-containing protein 3
KeywordsTRANSCRIPTION / inhibitor / bromodomain / epigenetics
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
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. ...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
Physachenolide C / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsHorton, N.C. / Chapman, E. / Sivinski, J. / Zerio, C. / Ghadirian, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Physachenolide C is a Potent, Selective BET Inhibitor.
Authors: Zerio, C.J. / Sivinski, J. / Wijeratne, E.M.K. / Xu, Y.M. / Ngo, D.T. / Ambrose, A.J. / Villa-Celis, L. / Ghadirian, N. / Clarkson, M.W. / Zhang, D.D. / Horton, N.C. / Gunatilaka, A.A.L. / ...Authors: Zerio, C.J. / Sivinski, J. / Wijeratne, E.M.K. / Xu, Y.M. / Ngo, D.T. / Ambrose, A.J. / Villa-Celis, L. / Ghadirian, N. / Clarkson, M.W. / Zhang, D.D. / Horton, N.C. / Gunatilaka, A.A.L. / Fromme, R. / Chapman, E.
History
DepositionSep 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
K: Bromodomain-containing protein 3
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Bromodomain-containing protein 3
D: Bromodomain-containing protein 3
E: Bromodomain-containing protein 3
F: Bromodomain-containing protein 3
G: Bromodomain-containing protein 3
H: Bromodomain-containing protein 3
I: Bromodomain-containing protein 3
J: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,83428
Polymers144,60811
Non-polymers6,22617
Water1,27971
1
K: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
F: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
G: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
H: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
I: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7283
Polymers13,1461
Non-polymers5822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
J: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6932
Polymers13,1461
Non-polymers5471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.448, 158.535, 293.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 309 or (resid 310 and (name...
d_2ens_1(chain "B" and (resid 309 or (resid 310 and (name...
d_3ens_1(chain "C" and (resid 309 or (resid 310 and (name...
d_4ens_1(chain "D" and (resid 309 or (resid 310 and (name...
d_5ens_1(chain "E" and (resid 309 or (resid 310 and (name...
d_6ens_1(chain "F" and (resid 309 or (resid 310 and (name...
d_7ens_1(chain "G" and (resid 309 or (resid 310 and (name...
d_8ens_1(chain "H" and (resid 309 or (resid 310 and (name...
d_9ens_1(chain "I" and (resid 309 or (resid 310 and (name...
d_10ens_1(chain "J" and (resid 309 through 312 or (resid 313...
d_11ens_1(chain "K" and (resid 309 or (resid 310 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPROA1 - 108
d_21ens_1SERPROB1 - 108
d_31ens_1SERPROC1 - 108
d_41ens_1SERPROD1 - 108
d_51ens_1SERPROE2 - 109
d_61ens_1SERPROF1 - 108
d_71ens_1SERPROG1 - 108
d_81ens_1SERPROH1 - 108
d_91ens_1SERPROI1 - 108
d_101ens_1SERPROJ1 - 108
d_111ens_1SERPROK1 - 108

NCS oper:
IDCodeMatrixVector
1given(-0.967952648823, 0.249625658921, -0.0274718045599), (-0.250922645713, -0.965812681566, 0.0651436105463), (-0.0102711005223, 0.0699492282648, 0.997497674162)47.8729404234, 80.7998494501, 52.1147938977
2given(0.844581559532, -0.524340565757, 0.108392621521), (-0.528220115233, -0.849064500148, 0.00854309374756), (0.0875528364028, -0.0644705024709, -0.994071453744)54.7364890962, 78.2966582985, -105.924370635
3given(-0.437012946597, 0.899437063678, 0.00571427938004), (0.899450089126, 0.436980187693, 0.006152457624), (0.00303672154371, 0.00782841273275, -0.999964746517)-0.460003317798, 0.668952766322, -66.3143023027
4given(0.63902606648, -0.76901670146, 0.0160934531738), (0.766124864487, 0.638208858553, 0.0757769416131), (-0.0685447180663, -0.036093846297, 0.996994912667)0.116615345819, 3.55409816199, 14.3365016201
5given(0.167997692316, -0.981540356023, 0.0914073567906), (-0.984887471148, -0.171082380509, -0.0269719901792), (0.0421122850388, -0.0854947283666, -0.995448244195)53.1989397545, 77.4877869792, -118.867152403
6given(-0.829466519171, -0.557974253854, -0.0254955998344), (0.55251839976, -0.826338176031, 0.109035025384), (-0.0819067243963, 0.0763541149511, 0.993710892377)46.7848299223, 83.0041097954, 39.506698671
7given(0.41563379029, 0.907232387451, 0.0646370445624), (0.907113680756, -0.41865951236, 0.0432317348259), (0.0662821435566, 0.0406645775997, -0.996971950244)2.49001789819, 2.07687787087, -80.3816545792
8given(-0.142949314542, -0.989711658275, -0.00602718400837), (0.984136167557, -0.14278528475, 0.105301311319), (-0.105078528629, 0.00912118050222, 0.994422096942)98.6515921838, 4.58774027046, 27.1222012538
9given(0.628479579629, 0.775361878194, -0.0618657888811), (-0.777825152397, 0.626364618401, -0.0515305454513), (-0.00120427926084, 0.0805066622079, 0.996753343135)-1.53402021018, -1.68668762248, -14.6323572884
10given(0.956413332372, 0.262001915317, 0.128951673242), (0.26050018664, -0.965047688188, 0.0286812182944), (0.131959048277, 0.00616083538171, -0.991236023198)6.17639648132, 1.2354571067, -94.3197207858

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Components

#1: Protein
Bromodomain-containing protein 3 / RING3-like protein


Mass: 13146.177 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Chemical
ChemComp-8L6 / Physachenolide C


Mass: 546.649 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C30H42O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.03 Å3/Da / Density % sol: 69.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium chloride 0.1 M BIS-TRIS pH 6.5 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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.89→39.49 Å / Num. obs: 53287 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 55.77 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05044 / Rpim(I) all: 0.05044 / Rrim(I) all: 0.07134 / Net I/σ(I): 7.67
Reflection shellResolution: 2.89→2.993 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3034 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 5273 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.3034 / Rrim(I) all: 0.4291 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX1.19_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Blu-Icedata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oo1

2oo1


Resolution: 2.89→39.49 Å / SU ML: 0.3791 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 1995 3.75 %
Rwork0.2071 51241 -
obs0.2084 53236 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.95 Å2
Refinement stepCycle: LAST / Resolution: 2.89→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9478 0 435 71 9984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009510248
X-RAY DIFFRACTIONf_angle_d1.186214085
X-RAY DIFFRACTIONf_chiral_restr0.07061465
X-RAY DIFFRACTIONf_plane_restr0.00951789
X-RAY DIFFRACTIONf_dihedral_angle_d16.30263670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EX-RAY DIFFRACTIONTorsion NCS0.394033399352
ens_1d_3EX-RAY DIFFRACTIONTorsion NCS0.451084782878
ens_1d_4EX-RAY DIFFRACTIONTorsion NCS0.309352760894
ens_1d_5EX-RAY DIFFRACTIONTorsion NCS0.398932958066
ens_1d_6EX-RAY DIFFRACTIONTorsion NCS0.418643940463
ens_1d_7EX-RAY DIFFRACTIONTorsion NCS0.418444572586
ens_1d_8EX-RAY DIFFRACTIONTorsion NCS0.417768500383
ens_1d_9EX-RAY DIFFRACTIONTorsion NCS0.401618513901
ens_1d_10EX-RAY DIFFRACTIONTorsion NCS0.397733411259
ens_1d_11EX-RAY DIFFRACTIONTorsion NCS0.428834710119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.35691390.30093613X-RAY DIFFRACTION99.81
2.96-3.040.33271420.26943633X-RAY DIFFRACTION99.89
3.04-3.130.30751410.24573625X-RAY DIFFRACTION99.97
3.13-3.230.28371410.22733620X-RAY DIFFRACTION99.95
3.23-3.350.31741400.2233618X-RAY DIFFRACTION100
3.35-3.480.31381430.25033647X-RAY DIFFRACTION99.89
3.48-3.640.25181410.21563633X-RAY DIFFRACTION99.97
3.64-3.830.24241420.19463610X-RAY DIFFRACTION99.87
3.83-4.070.25541420.20693666X-RAY DIFFRACTION99.74
4.07-4.390.20331420.18213636X-RAY DIFFRACTION100
4.39-4.830.18321430.16293681X-RAY DIFFRACTION100
4.83-5.520.19691450.17913702X-RAY DIFFRACTION100
5.52-6.950.22981440.22443707X-RAY DIFFRACTION99.97
6.95-39.490.20791500.19933850X-RAY DIFFRACTION99.5

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