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- PDB-2nxb: Crystal structure of human Bromodomain containing protein 3 (BRD3) -

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Basic information

Entry
Database: PDB / ID: 2nxb
TitleCrystal structure of human Bromodomain containing protein 3 (BRD3)
ComponentsBromodomain-containing protein 3
KeywordsSIGNALING PROTEIN / BRD3 / bromodomain containing protein 3 / ORFX / RING3 like gene / RING3L / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / : / protein localization to chromatin / molecular condensate scaffold activity / histone binding ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / : / protein localization to chromatin / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsFilippakopoulos, P. / Bullock, A. / Cooper, C. / Keates, K. / Berridge, G. / Pike, A. / Bunkoczi, G. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. ...Filippakopoulos, P. / Bullock, A. / Cooper, C. / Keates, K. / Berridge, G. / Pike, A. / Bunkoczi, G. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / von Delft, F. / 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
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 11, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 3
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,63110
Polymers29,1742
Non-polymers4578
Water4,990277
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7344
Polymers14,5871
Non-polymers1473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8976
Polymers14,5871
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.504, 61.840, 84.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14586.843 Da / Num. of mol.: 2 / Fragment: bromo 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-R3 / References: UniProt: Q15059
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20M KSCN, 0.1M BTPop, 20% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 10.2 / Number: 328713 / Rmerge(I) obs: 0.084 / Χ2: 1.05 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 54074 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.025099.910.0511.0038.9
2.393.0210010.0980.9989.3
2.092.3910010.1571.1119.3
1.92.0910010.2541.0898.6
1.761.910010.0891.1864.1
1.661.7610010.1151.1524.1
1.581.6610010.151.1154
1.511.5810010.21.0484
1.451.5110010.2710.9644
1.41.4510010.3980.9134
ReflectionResolution: 1.4→50 Å / Num. all: 54074 / Num. obs: 54074 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 10.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.398 / Rsym value: 0.398 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å49.91 Å
Translation3.5 Å49.91 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1X0J

1x0j


Resolution: 1.4→49.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.773 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18479 2748 5.1 %RANDOM
Rwork0.16761 ---
obs0.16848 51261 99.88 %-
all-54073 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.171 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1899 0 29 277 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222095
X-RAY DIFFRACTIONr_bond_other_d0.0010.021408
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9462836
X-RAY DIFFRACTIONr_angle_other_deg2.09133454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03725.75899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44815356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.234153
X-RAY DIFFRACTIONr_chiral_restr0.0710.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022277
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined0.2220.2458
X-RAY DIFFRACTIONr_nbd_other0.1740.21366
X-RAY DIFFRACTIONr_nbtor_refined0.1950.2998
X-RAY DIFFRACTIONr_nbtor_other0.090.2856
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5431.51247
X-RAY DIFFRACTIONr_mcbond_other0.1591.5478
X-RAY DIFFRACTIONr_mcangle_it0.96222036
X-RAY DIFFRACTIONr_scbond_it1.6683892
X-RAY DIFFRACTIONr_scangle_it2.4894.5799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 192 -
Rwork0.257 3709 -
obs--98.61 %
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)
110.5328-2.8583.61223.7673-2.9114.80910.32770.2463-0.5181-0.5494-0.18180.11390.50610.1515-0.1459-0.02120.0261-0.0488-0.1026-0.0188-0.0978-3.1861-24.99033.5352
23.7047-0.80560.86582.253-0.40192.23570.03160.15620.3333-0.3707-0.1176-0.1759-0.04010.39290.086-0.03690.0442-0.0131-0.02070.0146-0.1152-2.7194-4.7014-3.1466
32.0406-2.5838-0.19796.08360.6141.33180.07610.1010.1295-0.1657-0.13-0.2269-0.050.08290.054-0.11480.01320.0013-0.08340.0168-0.13791.4439-8.89424.8584
40.43951.1251-0.115111.6037-6.51925.9886-0.17430.10170.0513-0.09730.29960.3548-0.0056-0.3633-0.1254-0.1161-0.0028-0.0132-0.0798-0.001-0.1078-11.0573-10.44357.2129
512.8728-17.16920.599526.7985-1.96227.0520.43650.3316-0.937-0.2389-0.31530.93760.41050.0531-0.1211-0.0609-0.0064-0.0534-0.0879-0.0374-0.0486-6.9134-28.358411.1801
63.87650.2478-0.59481.5912-0.13111.69840.03850.0030.1050.2037-0.0303-0.0163-0.17250.0324-0.0082-0.0442-0.0093-0.0136-0.1236-0.0077-0.1403-3.28394.340121.4754
71.3017-2.2688-0.47417.79832.3611.9064-0.0617-0.2939-0.19540.63770.11050.48480.09720.0461-0.0488-0.0245-0.00770.0626-0.04940.0103-0.0579-13.5112-13.130228.4034
81.63070.6930.53841.92040.19022.20010.0250.0021-0.0520.1177-0.03450.0049-0.0202-0.01670.0095-0.1130.0025-0.0075-0.1413-0.0021-0.1242-3.1549-1.640921.015
95.02312.7935-0.24315.6804-0.23032.03570.0357-0.0870.01860.1702-0.03590.58080.0138-0.27680.0002-0.12250.00760.0179-0.1069-0.0155-0.059-17.2025-10.423219.5703
104.72035.0495-2.852219.7149-6.35935.70010.02260.12930.30660.1606-0.02330.4464-0.2979-0.05680.0007-0.08440.0558-0.0073-0.08070.0063-0.0068-18.39733.698718.5701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 4613 - 25
2X-RAY DIFFRACTION2AA47 - 7326 - 52
3X-RAY DIFFRACTION3AA74 - 12353 - 102
4X-RAY DIFFRACTION4AA124 - 138103 - 117
5X-RAY DIFFRACTION5AA139 - 144118 - 123
6X-RAY DIFFRACTION6BB23 - 512 - 30
7X-RAY DIFFRACTION7BB52 - 7731 - 56
8X-RAY DIFFRACTION8BB78 - 10157 - 80
9X-RAY DIFFRACTION9BB102 - 12481 - 103
10X-RAY DIFFRACTION10BB125 - 143104 - 122

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