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- PDB-3hme: Crystal structure of human bromodomain containing 9 isoform 1 (BRD9) -

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Basic information

Entry
Database: PDB / ID: 3hme
TitleCrystal structure of human bromodomain containing 9 isoform 1 (BRD9)
ComponentsBromodomain-containing protein 9
KeywordsSIGNALING PROTEIN / BRD9 / bromodomain containing 9 isoform 1 / LAVS3040 / PRO9856 / Rhabdomyosarcoma antigen MU-RMS-40.8 / Sarcoma antigen NY-SAR-29 / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
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
Bromodomain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsFilippakopoulos, P. / Eswaran, J. / Keates, T. / Picaud, S. / Roos, A. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. ...Filippakopoulos, P. / Eswaran, J. / Keates, T. / Picaud, S. / Roos, A. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)28,5002
Polymers28,5002
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-11 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.264, 124.586, 30.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLNGLN1AA26 - 3715 - 26
21GLNGLNGLNGLN1BB26 - 3715 - 26
12ARGARGPROPRO4AA38 - 6427 - 53
22ARGARGPROPRO4BB38 - 6427 - 53
13METMETLEULEU2AA65 - 11454 - 103
23METMETLEULEU2BB65 - 11454 - 103
14HISHISLYSLYS4AA115 - 130104 - 119
24HISHISLYSLYS4BB115 - 130104 - 119

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Components

#1: Protein Bromodomain-containing protein 9 / BRD9 / Rhabdomyosarcoma antigen MU-RMS-40.8


Mass: 14249.763 Da / Num. of mol.: 2 / Fragment: Bromodomain, UNP RESIDUES 14-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD9, UNQ3040/PRO9856 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9H8M2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Mosaicity: 0.63 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25.5% PEG 3350, 0.17M (NH4)2SO4, 15% glyc, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.23→35.62 Å / Num. all: 13809 / Num. obs: 13436 / % possible obs: 97.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.2
Reflection shellResolution: 2.23→2.35 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1608 / Rsym value: 0.598 / % possible all: 81.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.59 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.63 Å
Translation2.5 Å35.63 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 14108
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.06-10021.50.822503
5.52-7.06400.791505
4.79-5.5245.80.773508
4.32-4.7940.10.834508
4.01-4.3242.30.795504
3.75-4.0141.40.802501
3.56-3.7541.90.792516
3.39-3.5639.30.784514
3.26-3.3942.90.766514
3.14-3.2644.30.747510
3.04-3.1445.90.731511
2.94-3.0446.30.693539
2.86-2.9444.90.764546
2.78-2.8642.50.754547
2.71-2.7849.70.736580
2.64-2.7145.10.76590
2.58-2.6446.30.797604
2.52-2.5846.10.787581
2.47-2.5247.10.755643
2.42-2.4745.70.751651
2.37-2.4250.20.784652
2.32-2.37460.809646
2.28-2.3245.20.814668
2.21-2.2849.70.6891267

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Processing

Software
NameVersionClassificationNB
SCALA3.3.2data scaling
PHASER2.1.2phasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.23→35.62 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.205 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.835 / SU B: 14.676 / SU ML: 0.165 / SU R Cruickshank DPI: 0.306 / SU Rfree: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.263 680 5.1 %RANDOM
Rwork0.213 ---
all0.216 13756 --
obs0.216 13387 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 84.75 Å2 / Biso mean: 15.001 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2---2.75 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.23→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 0 111 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221876
X-RAY DIFFRACTIONr_bond_other_d0.0010.021318
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9642525
X-RAY DIFFRACTIONr_angle_other_deg0.86833213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84923.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20915346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8521510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_mcbond_it3.96331143
X-RAY DIFFRACTIONr_mcbond_other1.5923450
X-RAY DIFFRACTIONr_mcangle_it5.66151843
X-RAY DIFFRACTIONr_scbond_it7.8498733
X-RAY DIFFRACTIONr_scangle_it9.93811680
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
483TIGHT POSITIONAL0.220.05
942MEDIUM POSITIONAL0.390.5
483TIGHT THERMAL1.310.5
942MEDIUM THERMAL1.362
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 37 -
Rwork0.429 603 -
all-640 -
obs--64 %
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)
11.02411.52850.43247.95750.78270.3635-0.097-0.0224-0.1909-0.4570.2481-1.3346-0.18480.3682-0.1510.3191-0.28690.16060.7915-0.11290.427760.57369.348324.5553
21.76630.9508-0.47683.57021.08491.6026-0.070.14370.1147-0.97090.2375-0.0654-0.35990.5341-0.16750.4134-0.11190.04290.3571-0.01320.184153.81513.240720.6252
30.2596-0.3708-0.161111.4437-1.95590.7450.0952-0.01870.19080.0460.1181-0.0391-0.21410.204-0.21330.2169-0.12560.06390.2323-0.02410.249249.76214.264730.0138
44.5563.4180.48299.59890.73152.9557-0.22020.1793-0.4892-0.19220.1101-0.68540.56860.10010.11010.20670.06990.11780.08610.0380.238866.75335.680822.4959
51.98581.09540.23613.6968-0.31121.5255-0.1347-0.0819-0.17440.1901-0.0252-0.13620.16440.05620.15990.1671-0.0010.05620.13590.01950.205464.753747.029226.3259
66.89456.2369-0.424110.0145-2.23962.1478-0.18820.1891-0.1703-0.45110.24720.05480.5306-0.0959-0.0590.2591-0.03810.0610.1108-0.00840.131159.485740.018414.8731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 54
2X-RAY DIFFRACTION2A55 - 105
3X-RAY DIFFRACTION3A106 - 134
4X-RAY DIFFRACTION4B23 - 49
5X-RAY DIFFRACTION5B50 - 103
6X-RAY DIFFRACTION6B104 - 134

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