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- PDB-5twx: Crystal Structure of BRD9 bromodomain -

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Basic information

Entry
Database: PDB / ID: 5twx
TitleCrystal Structure of BRD9 bromodomain
ComponentsBromodomain-containing protein 9
KeywordsTRANSCRIPTION / bromodomain / inhibitor / chemical degradation
Function / homology
Function and homology information


GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II ...GBAF complex / SWI/SNF complex / positive regulation of stem cell population maintenance / negative regulation of cell differentiation / lysine-acetylated histone binding / nucleic acid binding / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
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-7P7 / Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands.
Authors: Remillard, D. / Buckley, D.L. / Paulk, J. / Brien, G.L. / Sonnett, M. / Seo, H.S. / Dastjerdi, S. / Wuhr, M. / Dhe-Paganon, S. / Armstrong, S.A. / Bradner, J.E.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 9
B: Bromodomain-containing protein 9
C: Bromodomain-containing protein 9
D: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7328
Polymers55,2324
Non-polymers3,5004
Water70339
1
A: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6832
Polymers13,8081
Non-polymers8751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6832
Polymers13,8081
Non-polymers8751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6832
Polymers13,8081
Non-polymers8751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6832
Polymers13,8081
Non-polymers8751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-33 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.260, 75.260, 344.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 137 through 144 or (resid 145...
21(chain B and (resid 137 through 144 or (resid 145...
31(chain C and (resid 137 through 144 or (resid 145...
41(chain D and (resid 137 through 149 or resid 151...

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
11GLUGLULEULEU(chain A and (resid 137 through 144 or (resid 145...AA137 - 1448 - 15
12LEULEUGLUGLU(chain A and (resid 137 through 144 or (resid 145...AA145 - 14616 - 17
13GLUGLU7P77P7(chain A and (resid 137 through 144 or (resid 145...AA - E137 - 40008
14GLUGLU7P77P7(chain A and (resid 137 through 144 or (resid 145...AA - E137 - 40008
15GLUGLU7P77P7(chain A and (resid 137 through 144 or (resid 145...AA - E137 - 40008
16GLUGLU7P77P7(chain A and (resid 137 through 144 or (resid 145...AA - E137 - 40008
21GLUGLULEULEU(chain B and (resid 137 through 144 or (resid 145...BB137 - 1448 - 15
22LEULEUGLUGLU(chain B and (resid 137 through 144 or (resid 145...BB145 - 14616 - 17
23GLUGLU7P77P7(chain B and (resid 137 through 144 or (resid 145...BB - F137 - 40008
24GLUGLU7P77P7(chain B and (resid 137 through 144 or (resid 145...BB - F137 - 40008
25GLUGLU7P77P7(chain B and (resid 137 through 144 or (resid 145...BB - F137 - 40008
26GLUGLU7P77P7(chain B and (resid 137 through 144 or (resid 145...BB - F137 - 40008
31GLUGLULEULEU(chain C and (resid 137 through 144 or (resid 145...CC137 - 1448 - 15
32LEULEUGLUGLU(chain C and (resid 137 through 144 or (resid 145...CC145 - 14616 - 17
33GLUGLU7P77P7(chain C and (resid 137 through 144 or (resid 145...CC - G137 - 40008
34GLUGLU7P77P7(chain C and (resid 137 through 144 or (resid 145...CC - G137 - 40008
35GLUGLU7P77P7(chain C and (resid 137 through 144 or (resid 145...CC - G137 - 40008
36GLUGLU7P77P7(chain C and (resid 137 through 144 or (resid 145...CC - G137 - 40008
41GLUGLULEULEU(chain D and (resid 137 through 149 or resid 151...DD137 - 1498 - 20
42GLNGLNGLNGLN(chain D and (resid 137 through 149 or resid 151...DD151 - 15322 - 24
43LYSLYSALAALA(chain D and (resid 137 through 149 or resid 151...DD155 - 16226 - 33
44PROPROALAALA(chain D and (resid 137 through 149 or resid 151...DD164 - 16835 - 39
45ALAALALYSLYS(chain D and (resid 137 through 149 or resid 151...DD170 - 22741 - 98
46ILEILELEULEU(chain D and (resid 137 through 149 or resid 151...DD229 - 230100 - 101
47ALAALAPHEPHE(chain D and (resid 137 through 149 or resid 151...DD232 - 234103 - 105
48METMETLEULEU(chain D and (resid 137 through 149 or resid 151...DD236 - 244107 - 115

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Components

#1: Protein
Bromodomain-containing protein 9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 13807.977 Da / Num. of mol.: 4 / Fragment: UNP residues 134-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H8M2
#2: Chemical
ChemComp-7P7 / N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide


Mass: 874.978 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H46N6O11S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.75 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.55→64.04 Å / Num. obs: 19982 / % possible obs: 100 % / Redundancy: 13 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.143 / Net I/σ(I): 15.3 / Num. measured all: 260441
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.55-2.5914.31.6141009890.5262.03100
6.92-64.0611.647.11349611650.0110.03899.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YYD

4yyd


Resolution: 2.55→64.04 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 950 4.76 %
Rwork0.2327 18988 -
obs0.235 19938 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.83 Å2 / Biso mean: 74.0504 Å2 / Biso min: 34.3 Å2
Refinement stepCycle: final / Resolution: 2.55→64.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 221 39 3626
Biso mean--68.7 52.16 -
Num. residues----442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053737
X-RAY DIFFRACTIONf_angle_d1.4785085
X-RAY DIFFRACTIONf_chiral_restr0.045527
X-RAY DIFFRACTIONf_plane_restr0.005635
X-RAY DIFFRACTIONf_dihedral_angle_d11.2412199
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1615X-RAY DIFFRACTION15.769TORSIONAL
12B1615X-RAY DIFFRACTION15.769TORSIONAL
13C1615X-RAY DIFFRACTION15.769TORSIONAL
14D1615X-RAY DIFFRACTION15.769TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.68450.38381340.332626422776100
2.6845-2.85260.33211260.29726172743100
2.8526-3.07290.3541230.286426512774100
3.0729-3.38210.34451370.265626752812100
3.3821-3.87150.27331260.22527082834100
3.8715-4.87740.24681400.198427422882100
4.8774-64.06010.24841640.21182953311799
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)
14.1825-0.6565-1.22317.19460.96172.3108-0.4085-0.74650.06930.71620.1736-1.4390.2971-0.1895-0.02030.342-0.02950.05520.6482-0.0610.5577-34.7398-12.2464-13.4036
25.0305-1.01954.7326.6204-5.08127.0608-0.5613-0.57023.32441.7776-0.47920.1176-1.2388-0.2761-0.29930.64020.03450.22160.81970.06120.9542-46.6807-1.8963-4.8207
33.69820.59690.41653.98071.60312.0775-0.4107-0.6477-1.01231.0831-0.230.47851.0531-0.43830.25340.43880.03770.07450.72450.0020.7628-55.3671-10.0984-5.1239
44.4551-1.0166-0.00074.18821.49642.1009-0.6504-0.5011-0.443-0.19140.30320.85870.17740.0670.28270.46020.02530.01570.9128-0.04390.7826-59.2843-13.0572-12.5796
54.0866-1.18820.72313.32170.77181.3136-0.9507-0.0702-0.47040.08161.07610.86170.12250.07790.05710.34460.01530.10210.6534-0.05590.7257-42.9146-16.8361-10.6438
61.8260.35672.17512.9366-0.62712.954-0.4967-0.1707-1.67350.7852-0.4148-0.40752.68171.34170.23221.0329-0.0220.12140.64-0.17650.6103-40.4284-21.8477-17.5283
74.17890.36620.06114.3663-1.1894.355-0.2610.881-0.085-0.24090.32610.2813-0.3567-0.2487-0.14590.36350.0749-0.02770.8059-0.12960.4725-49.565-9.6928-18.5495
85.72030.7806-5.02722.107-0.62052.60460.10690.57991.033-0.0660.42130.3739-0.429-0.2639-0.37870.41730.0864-0.0110.7396-0.01490.5745-45.287-0.8949-18.3406
91.34231.46010.59611.8981-0.01793.4535-0.7505-0.330.4327-0.7291-0.61181.0732-1.53350.48230.10770.6184-0.05020.03980.9277-0.11180.7076-23.3695-2.0151-31.1853
105.6949-2.12624.74522.9629-1.62183.3141-0.2061-1.44070.01830.27290.4537-0.1042-0.1208-1.0732-0.1890.34050.01680.06650.7921-0.12260.5241-20.3649-8.9177-11.258
115.7713-0.26932.05892.00990.46034.7522-0.2482-0.49960.28090.0540.0999-0.81950.01410.47750.12750.4063-0.04220.05050.741-0.15980.5961-8.2853-7.723-13.8832
125.2584-1.89031.15614.62780.00184.4050.0512-0.129-0.5375-0.1607-0.0063-0.20520.26210.0110.09960.4426-0.00650.1060.4327-0.05490.4748-18.4173-18.1436-18.3278
134.00382.3865.06245.39633.85798.39160.1728-0.3492-1.17720.13251.0591-1.41920.20572.8862-0.47290.4134-0.03510.11371.52510.25680.9141-32.7632-17.829714.269
147.2682-0.0049-1.95236.0647-1.22275.74420.61430.4940.5926-0.7378-1.0146-1.0274-0.0503-0.02050.29580.6084-0.0405-0.01131.03170.0970.5449-46.7473-14.35614.643
153.583-1.56740.12462.1217-0.18942.9701-0.4094-0.7899-0.32670.1005-0.040.34790.0010.30560.2530.57920.00760.06571.02290.14120.6365-48.9-13.539915.4176
166.8403-4.78461.29965.0293-1.93212.31750.3113-0.131-2.383-0.7157-0.25350.81050.60990.79640.19370.683-0.06830.08290.95480.17340.924-49.6587-22.97612.771
173.9625-2.4384.67443.1704-1.52374.6940.3986-1.1554-1.6403-0.37970.0123-0.67910.24990.0754-0.42990.64250.01820.03581.05930.40331.3252-41.2923-28.09469.3122
182.1087-2.4768-1.84265.419-0.58314.6675-0.6128-2.3387-0.5911-0.73450.24140.6985-0.0311-0.0261-0.27460.43670.0853-0.01351.57860.08820.9706-16.5717-18.83299.5276
193.93961.85691.94551.6532-0.80345.67051.3556-1.30530.44520.5215-1.2390.75110.61270.3801-0.67550.7254-0.26860.00172.25790.09920.97754.9184-16.98088.4059
200.63890.7613-0.4271.8019-0.9460.3553-0.63510.1079-0.1031-0.4933-0.2446-0.68690.99840.78420.64160.55070.09710.06961.96950.22261.2945-9.9467-24.04687.4137
210.5637-1.10050.37662.8226-1.52151.0385-1.1804-1.4779-2.17660.12481.2820.92661.91982.6496-0.56960.4910.2378-0.11952.27290.40021.3266-9.8388-25.162214.6376
224.5085-3.02811.33745.4483-2.07147.4292-1.2398-1.5635-0.46920.39041.123-1.36930.13410.8160.67010.68290.0441-0.05372.3117-0.48531.2399-4.3568-12.403820.1191
239.4774-0.94191.48651.58061.45431.91130.5308-0.0975-0.44630.66120.3970.2567-0.0631.3929-0.58910.8780.10380.13742.06280.44530.826-22.9152-22.969623.1094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 137 through 155 )A137 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 160 )A156 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 170 )A161 - 170
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 182 )A171 - 182
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 191 )A183 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 197 )A192 - 197
7X-RAY DIFFRACTION7chain 'A' and (resid 198 through 215 )A198 - 215
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 244 )A216 - 244
9X-RAY DIFFRACTION9chain 'A' and (resid 245 through 250 )A245 - 250
10X-RAY DIFFRACTION10chain 'B' and (resid 137 through 165 )B137 - 165
11X-RAY DIFFRACTION11chain 'B' and (resid 166 through 220 )B166 - 220
12X-RAY DIFFRACTION12chain 'B' and (resid 221 through 247 )B221 - 247
13X-RAY DIFFRACTION13chain 'C' and (resid 137 through 155 )C137 - 155
14X-RAY DIFFRACTION14chain 'C' and (resid 156 through 165 )C156 - 165
15X-RAY DIFFRACTION15chain 'C' and (resid 166 through 197 )C166 - 197
16X-RAY DIFFRACTION16chain 'C' and (resid 198 through 220 )C198 - 220
17X-RAY DIFFRACTION17chain 'C' and (resid 221 through 244 )C221 - 244
18X-RAY DIFFRACTION18chain 'D' and (resid 137 through 167 )D137 - 167
19X-RAY DIFFRACTION19chain 'D' and (resid 168 through 176 )D168 - 176
20X-RAY DIFFRACTION20chain 'D' and (resid 177 through 191 )D177 - 191
21X-RAY DIFFRACTION21chain 'D' and (resid 192 through 215 )D192 - 215
22X-RAY DIFFRACTION22chain 'D' and (resid 216 through 231 )D216 - 231
23X-RAY DIFFRACTION23chain 'D' and (resid 232 through 245 )D232 - 245

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