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- PDB-6v16: Crystal structure of the bromodomain of human BRD7 bound to TP472 -

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Basic information

Entry
Database: PDB / ID: 6v16
TitleCrystal structure of the bromodomain of human BRD7 bound to TP472
ComponentsBromodomain-containing protein 7
KeywordsGENE REGULATION / BRD7 / non-BET / PBAF / mSWI/SNF
Function / homology
Function and homology information


histone H3K14ac reader activity / regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of double-strand break repair / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation ...histone H3K14ac reader activity / regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of double-strand break repair / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / Regulation of TP53 Activity through Acetylation / : / transcription initiation-coupled chromatin remodeling / regulation of mitotic cell cycle / positive regulation of cell differentiation / kinetochore / nuclear matrix / Wnt signaling pathway / p53 binding / transcription corepressor activity / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily ...Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Chem-QMG / Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKarim, M.R. / Chan, A. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.
Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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-containing protein 7
B: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7287
Polymers28,7892
Non-polymers9395
Water2,828157
1
A: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7903
Polymers14,3951
Non-polymers3952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9384
Polymers14,3951
Non-polymers5443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.084, 33.497, 76.561
Angle α, β, γ (deg.)90.000, 98.450, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 136 through 180 or resid 182...
21(chain B and (resid 136 through 180 or resid 182...

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
11LEULEUTHRTHR(chain A and (resid 136 through 180 or resid 182...AA136 - 1809 - 53
12LYSLYSLEULEU(chain A and (resid 136 through 180 or resid 182...AA182 - 20255 - 75
13CYSCYSALAALA(chain A and (resid 136 through 180 or resid 182...AA204 - 20777 - 80
14ILEILEHISHIS(chain A and (resid 136 through 180 or resid 182...AA209 - 22682 - 99
15GLYGLYGLNGLN(chain A and (resid 136 through 180 or resid 182...AA228 - 242101 - 115
16ILEILEILEILE(chain A and (resid 136 through 180 or resid 182...AA244117
21LEULEUTHRTHR(chain B and (resid 136 through 180 or resid 182...BB136 - 1809 - 53
22LYSLYSLEULEU(chain B and (resid 136 through 180 or resid 182...BB182 - 20255 - 75
23CYSCYSALAALA(chain B and (resid 136 through 180 or resid 182...BB204 - 20777 - 80
24ILEILEHISHIS(chain B and (resid 136 through 180 or resid 182...BB209 - 22682 - 99
25GLYGLYGLNGLN(chain B and (resid 136 through 180 or resid 182...BB228 - 242101 - 115
26ILEILEILEILE(chain B and (resid 136 through 180 or resid 182...BB244117

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bromodomain-containing protein 7 / 75 kDa bromodomain protein / Protein CELTIX-1


Mass: 14394.644 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: chemical compound / Gene: BRD7, BP75, CELTIX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q9NPI1

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Non-polymers , 5 types, 162 molecules

#2: Chemical ChemComp-QMG / 3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide


Mass: 333.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M (NH4)2SO4, 0.05 M Bis-tris (pH 6.5), and 30 % Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→46.573 Å / Num. obs: 18696 / % possible obs: 98.2 % / Redundancy: 3.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.048 / Rrim(I) all: 0.092 / Net I/σ(I): 8.8
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
1.9-1.943.50.169410611830.9530.1040.1993.795.7
9.11-46.5730.0985831960.9420.0640.11813.499.1

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Processing

Software
NameVersionClassification
PHENIX1.14-3260_3260refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PPA

6ppa


Resolution: 1.9→46.573 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 21.14
RfactorNum. reflection% reflection
Rfree0.2215 935 5 %
Rwork0.1879 --
obs0.1895 18694 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.67 Å2 / Biso mean: 31.5059 Å2 / Biso min: 12.17 Å2
Refinement stepCycle: final / Resolution: 1.9→46.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 68 157 2085
Biso mean--30.07 33.24 -
Num. residues----227
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A594X-RAY DIFFRACTION0.862TORSIONAL
12B594X-RAY DIFFRACTION0.862TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-2.00020.26851300.2256248096
2.0002-2.12550.26141300.2082247497
2.1255-2.28960.28241310.2039247798
2.2896-2.520.21811340.198253298
2.52-2.88460.21341330.1961253999
2.8846-3.63410.2081370.18142601100
3.6341-46.5730.20191400.16942656100
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)
13.6221-2.75230.51062.78030.98353.0942-0.1985-1.4153-0.47460.67010.20210.12780.32870.07220.02070.224-0.02010.01410.34420.12480.408360.56133.733791.9506
28.9285-1.0905-0.26214.4016-1.18512.53890.0510.1475-0.0455-0.21740.08190.160.1191-0.1935-0.04410.1213-0.04180.01670.12560.02360.145642.64269.942981.5857
32.2783-2.91360.8936.57990.9771.89870.028-0.4006-0.8055-0.18220.15640.3130.5144-0.2912-0.26520.2258-0.03070.01370.13980.08620.371552.52550.710987.4777
43.3917-0.51920.4580.37510.60361.3605-0.0970.1804-0.3225-0.06640.1106-0.09690.116-0.0486-0.08480.1611-0.02020.05250.13010.02770.242955.36256.524779.6232
50.68470.91710.73592.5119-1.94257.37910.08040.10630.6143-0.3743-0.24521.0331-0.742-0.61630.14240.23570.1910.0480.06740.12370.391542.604223.1377.4584
61.3879-1.0963-1.10842.4281-0.00772.64890.12490.01130.81160.1530.1577-0.4925-0.78780.20.34040.20120.03570.02610.00660.07970.402754.108219.463483.3455
74.8636-2.11542.47257.0208-4.64473.54470.23970.0606-0.2503-0.3054-0.2995-0.53060.61850.20040.07570.25740.03690.00330.2294-0.06430.282472.3393.392386.4305
83.6673.0655-4.63966.6247-3.72565.87450.07370.4497-0.0315-0.10570.29590.96930.5778-2.1214-0.47710.4019-0.2296-0.04020.61820.03550.315562.26842.232108.1047
95.74150.4551-2.64753.3496-0.4155.3529-0.22950.1574-0.0778-0.08990.1554-0.20980.24010.02150.10420.2094-0.0748-0.01560.11360.02820.115378.71195.238496.1124
101.170.1816-0.22190.4660.34480.40520.1894-0.2498-0.7924-0.23150.2705-0.08691.6784-0.4896-0.25650.6897-0.1726-0.06920.24360.08990.341569.8222-5.3087106.2174
113.7430.0062-0.23041.7153-0.7594.36450.0609-0.142-0.00260.6125-0.0725-0.0939-0.4510.0256-0.00510.2829-0.0424-0.02010.143-0.00490.107477.81718.4443105.7893
123.70262.6183-0.68353.8534-3.47164.56450.3618-0.24350.57370.7331-0.04440.4926-1.246-0.1714-0.24540.4855-0.00070.02920.1502-0.00480.21572.51414.9021105.6817
133.25892.1864-5.159.4939-4.2229.41130.6496-0.16630.14390.96720.01231.0137-0.9935-0.6406-0.64580.49150.07950.08990.48630.03970.394863.9923.0136121.0677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 132 through 150 )A132 - 150
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 177 )A151 - 177
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 186 )A178 - 186
4X-RAY DIFFRACTION4chain 'A' and (resid 187 through 210 )A187 - 210
5X-RAY DIFFRACTION5chain 'A' and (resid 211 through 215 )A211 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 231 )A216 - 231
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 249 )A232 - 249
8X-RAY DIFFRACTION8chain 'B' and (resid 136 through 150 )B136 - 150
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 177 )B151 - 177
10X-RAY DIFFRACTION10chain 'B' and (resid 178 through 192 )B178 - 192
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 215 )B193 - 215
12X-RAY DIFFRACTION12chain 'B' and (resid 216 through 231 )B216 - 231
13X-RAY DIFFRACTION13chain 'B' and (resid 232 through 244 )B232 - 244

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