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- PDB-5a7c: Crystal structure of the second bromodomain of human BRD3 in comp... -

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Basic information

Entry
Database: PDB / ID: 5a7c
TitleCrystal structure of the second bromodomain of human BRD3 in complex with compound
ComponentsBROMODOMAIN-CONTAINING PROTEIN 3
KeywordsDNA BINDING PROTEIN / BRD3 / BROMODOMAIN CONTAINING PROTEIN 3 / RING3-LIKE PROTEIN / BRD3 DOMAIN 2
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
N-(6-ACETAMIDOHEXYL)ACETAMIDE / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWelin, M. / Kimbung, R. / Diehl, C. / Hakansson, M. / Logan, D.T. / Walse, B.
CitationJournal: Cancer Res. / Year: 2016
Title: Cancer Differentiating Agent Hexamethylene Bisacetamide Inhibits Bet Bromodomain Proteins.
Authors: Nilsson, L.M. / Green, L.C. / Muralidharan, S.V. / Demir, D. / Welin, M. / Bhadury, J. / Logan, D.T. / Walse, B. / Nilsson, J.A.
History
DepositionJul 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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
C: BROMODOMAIN-CONTAINING PROTEIN 3
D: BROMODOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,34113
Polymers53,2304
Non-polymers1,1119
Water6,593366
1
A: BROMODOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6324
Polymers13,3071
Non-polymers3243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BROMODOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5703
Polymers13,3071
Non-polymers2622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BROMODOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5703
Polymers13,3071
Non-polymers2622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BROMODOMAIN-CONTAINING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5703
Polymers13,3071
Non-polymers2622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.365, 92.013, 64.898
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYMETMETAA306 - 4153 - 112
21GLYGLYMETMETBB306 - 4153 - 112
12LEULEUMETMETAA308 - 4155 - 112
22LEULEUMETMETCC308 - 4155 - 112
13LEULEUMETMETAA308 - 4155 - 112
23LEULEUMETMETDD308 - 4155 - 112
14LEULEUMETMETBB308 - 4155 - 112
24LEULEUMETMETCC308 - 4155 - 112
15LEULEUMETMETBB308 - 4155 - 112
25LEULEUMETMETDD308 - 4155 - 112
16LEULEUPROPROCC308 - 4165 - 113
26LEULEUPROPRODD308 - 4165 - 113

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(0.582, -0.679, 0.448), (-0.668, -0.713, -0.214), (0.464, -0.174, -0.868)-24.627, -18.204, 58.751
2given(0.582, -0.679, 0.448), (-0.668, -0.713, -0.214), (0.464, -0.174, -0.868)-24.627, -18.204, 58.751
3given(-0.668, 0.669, 0.327), (0.679, 0.727, -0.101), (-0.306, 0.155, -0.94)11.39, -30.85, 112.24

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Components

#1: Protein
BROMODOMAIN-CONTAINING PROTEIN 3 / RING3-LIKE PROTEIN


Mass: 13307.399 Da / Num. of mol.: 4 / Fragment: BROMO 2 DOMAIN, RESIDUES 306-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): T1R PRARE2 / References: UniProt: Q15059
#2: Chemical
ChemComp-5D4 / N-(6-ACETAMIDOHEXYL)ACETAMIDE


Mass: 200.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20N2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.89 Å3/Da / Density % sol: 57.5 % / Description: NONE
Crystal growpH: 7 / Details: 19% PEG 6000, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2015 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.56 Å / Num. obs: 47219 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.4 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S92

3s92


Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.846 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25558 2311 4.9 %RANDOM
Rwork0.22813 ---
obs0.22947 44884 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20.24 Å2
2---0.69 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 76 366 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193837
X-RAY DIFFRACTIONr_bond_other_d0.010.023646
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9745148
X-RAY DIFFRACTIONr_angle_other_deg1.50138423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9455439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64122.963189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8011528
X-RAY DIFFRACTIONr_chiral_restr0.090.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214235
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02907
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4941.7511765
X-RAY DIFFRACTIONr_mcbond_other1.4941.7521766
X-RAY DIFFRACTIONr_mcangle_it2.2912.6252213
X-RAY DIFFRACTIONr_mcangle_other2.2772.6252211
X-RAY DIFFRACTIONr_scbond_it2.532.0932071
X-RAY DIFFRACTIONr_scbond_other2.532.0932071
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.03132936
X-RAY DIFFRACTIONr_long_range_B_refined5.53114.744851
X-RAY DIFFRACTIONr_long_range_B_other5.5314.7434852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A134080.06
12B134080.06
21A134060.04
22C134060.04
31A132900.06
32D132900.06
41B131300.06
42C131300.06
51B133160.04
52D133160.04
61C133620.06
62D133620.06
LS refinement shellHighest resolution: 1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 158 -
Rwork0.402 3163 -
obs--94.72 %

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