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- PDB-6fgh: Crystal Structure of BAZ2A bromodomain in complex with 3-amino-2-... -

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Basic information

Entry
Database: PDB / ID: 6fgh
TitleCrystal Structure of BAZ2A bromodomain in complex with 3-amino-2-methylpyridine derivative 1
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / histone H4K16ac reader activity / rDNA heterochromatin formation / RNA polymerase I preinitiation complex assembly / chromatin silencing complex / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6RZ / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsDalle Vedove, A. / Marchand, J.-R. / Lolli, G. / Caflisch, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_169007 Switzerland
CitationJournal: ChemMedChem / Year: 2018
Title: Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains.
Authors: Dalle Vedove, A. / Spiliotopoulos, D. / D'Agostino, V.G. / Marchand, J.R. / Unzue, A. / Nevado, C. / Lolli, G. / Caflisch, A.
History
DepositionJan 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / 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 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6092
Polymers12,3811
Non-polymers2281
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.278, 95.278, 33.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2044-

HOH

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / hWALp3


Mass: 12380.919 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 1796-1899)
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF9
#2: Chemical ChemComp-6RZ / 2-methyl-~{N}-[(2~{R})-1-methylsulfonylpropan-2-yl]pyridin-3-amine


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.5 Å3/Da / Density % sol: 64.82 % / Mosaicity: 0.25 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.64 Å / Num. obs: 10275 / % possible obs: 99.9 % / Redundancy: 9.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.049 / Rrim(I) all: 0.154 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1610.41.2088160.7830.391.27100
8.91-47.649.30.0491570.9970.0170.05299.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.3.11data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MGJ

5mgj


Resolution: 2.1→41.257 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.06
RfactorNum. reflection% reflection
Rfree0.2155 559 5.45 %
Rwork0.1892 --
obs0.1907 10258 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.55 Å2 / Biso mean: 42.2562 Å2 / Biso min: 16.22 Å2
Refinement stepCycle: final / Resolution: 2.1→41.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 30 96 979
Biso mean--32.36 42.93 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006905
X-RAY DIFFRACTIONf_angle_d0.781221
X-RAY DIFFRACTIONf_chiral_restr0.045121
X-RAY DIFFRACTIONf_plane_restr0.005158
X-RAY DIFFRACTIONf_dihedral_angle_d6.27528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.31140.32081260.27532386251299
2.3114-2.64580.23881330.212724242557100
2.6458-3.33320.22041370.193624152552100
3.3332-41.26450.19041630.161624742637100
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)
10.3139-0.04720.07090.01660.03740.25890.0355-0.1237-0.17550.1504-0.1274-0.1370.2443-0.2433-0.04030.2524-0.15840.02560.2842-0.00790.3502-33.014820.1908-9.1219
20.00490.0135-0.05810.6226-0.62451.0647-0.02890.0689-0.0259-0.0971-0.05720.01530.1362-0.3307-0.02820.1498-0.01470.0010.5788-0.05070.2177-38.301336.8256-19.8772
30.11650.04540.07640.2439-0.20090.5856-0.2130.3332-0.1933-0.12580.0695-0.1760.0787-0.1244-0.05240.1848-0.12190.06050.3188-0.09930.2341-29.825628.1931-21.1449
40.1396-0.0566-0.4470.08260.05781.69610.0995-0.021-0.14310.1266-0.0501-0.0044-0.143-0.18060.06030.1143-0.0809-0.04050.27260.01350.2206-27.819534.7017-9.3747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1796 through 1810 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1811 through 1829 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1830 through 1872 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1873 through 1898 )A0

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