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- PDB-6v17: Crystal structure of the bromodomain of human BRD7 bound to I-BRD9 -

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Basic information

Entry
Database: PDB / ID: 6v17
TitleCrystal structure of the bromodomain of human BRD7 bound to I-BRD9
ComponentsBromodomain-containing protein 7
KeywordsGENE REGULATION / non-BET / bromodomain / PBAF / mSWI/SNF / BP75 / CELTIX1
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / regulation of mitotic cell cycle / positive regulation of cell differentiation / lysine-acetylated histone binding / kinetochore / Wnt signaling pathway / nuclear matrix / transcription corepressor activity / p53 binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / cell cycle / negative regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-H1B / Bromodomain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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)29,8205
Polymers28,7892
Non-polymers1,0313
Water57632
1
A: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9283
Polymers14,3951
Non-polymers5332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8922
Polymers14,3951
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Bromodomain-containing protein 7
hetero molecules

B: Bromodomain-containing protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8205
Polymers28,7892
Non-polymers1,0313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area1340 Å2
ΔGint-17 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.102, 64.749, 96.107
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 132 - 250 / Label seq-ID: 5 - 123

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#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) / Gene: BRD7, BP75, CELTIX1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: Q9NPI1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-H1B / N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide


Mass: 497.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22F3N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
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 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→64.75 Å / Num. obs: 16528 / % possible obs: 98.8 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Net I/σ(I): 7.5 / Num. measured all: 107062 / Scaling rejects: 372
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
2.05-2.114.80.648520810780.5680.3150.7232.286.7
8.94-64.755.40.07913542500.990.0360.08714.799.2

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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: 2.05→38.588 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2412 825 5 %
Rwork0.2091 --
obs0.2106 16484 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.06 Å2 / Biso mean: 46.1175 Å2 / Biso min: 16.83 Å2
Refinement stepCycle: final / Resolution: 2.05→38.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 67 32 2049
Biso mean--43.01 33.31 -
Num. residues----238
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A716X-RAY DIFFRACTION6.792TORSIONAL
12B716X-RAY DIFFRACTION6.792TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0501-2.17860.2891270.2708240993
2.1786-2.34680.3211350.25242575100
2.3468-2.58290.27191380.23562614100
2.5829-2.95650.28141390.23162631100
2.9565-3.72440.24511400.2072653100
3.7244-38.5880.18961460.1772777100
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)
12.01191.05361.39063.7452.73534.4162-0.20960.46640.09880.43590.394-1.630.02590.9129-0.4570.38810.0106-0.24380.6455-0.16280.788419.235-1.774-12.266
27.0066-1.6568-0.35586.16282.08434.98810.25680.8479-0.0737-0.5769-0.1043-0.4677-1.06130.5795-0.15020.3258-0.15090.0220.42270.05020.34677.932-0.781-29.163
34.98543.23730.87746.6353-0.127.9109-0.15450.4910.5606-0.31430.64420.0277-1.2890.3784-0.51290.4102-0.1281-0.1650.37260.06840.783415.7366.776-13.431
45.45091.61552.70484.99171.54773.30810.01060.0347-0.2280.62660.0419-0.25340.50740.5967-0.02160.25980.0407-0.05520.2347-0.00240.26647.752-8.484-16.262
56.23095.24514.60394.86543.49834.6718-0.2080.20780.42150.1348-0.17070.81180.0673-0.02560.44460.41230.0822-0.07350.5413-0.06490.356513.8242.9145.428
67.7690.1651-0.32924.0483.28957.3893-0.31150.2821-0.16450.11380.4394-0.75370.63951.0231-0.15970.3680.04830.07590.30990.00930.33340.858-2.4112.542
75.8772-1.1488-3.6353.18990.33866.7849-0.1529-0.052-0.1615-0.0164-0.0193-0.15790.33780.1430.08440.1833-0.0083-0.00890.1275-0.00230.21530.9242.69614.061
83.5653-0.9585-2.15691.12530.42733.56140.50051.3026-0.684-0.7395-1.66780.9649-0.5191-1.91181.06720.45680.0818-0.05330.7897-0.31550.469733.949-3.435-9.923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 132:160 )A132 - 160
2X-RAY DIFFRACTION2( CHAIN A AND RESID 161:177 )A161 - 177
3X-RAY DIFFRACTION3( CHAIN A AND RESID 178:192 )A178 - 192
4X-RAY DIFFRACTION4( CHAIN A AND RESID 193:233 )A193 - 233
5X-RAY DIFFRACTION5( CHAIN A AND RESID 234:250 )A234 - 250
6X-RAY DIFFRACTION6( CHAIN B AND RESID 132:150 )B132 - 150
7X-RAY DIFFRACTION7( CHAIN B AND RESID 151:231 )B151 - 231
8X-RAY DIFFRACTION8( CHAIN B AND RESID 232:250 )B232 - 250

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