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- PDB-6fkp: Crystal structure of BAZ2A PHD zinc finger in complex with H3 10-... -

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Basic information

Entry
Database: PDB / ID: 6fkp
TitleCrystal structure of BAZ2A PHD zinc finger in complex with H3 10-mer AA mutant peptide
Components
  • ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
  • Bromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION / PHD zinc finger / bromodomain / BAZ2A / histone / epigenetic / H3
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / 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 / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsAmato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.
Authors: Amato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
B: Bromodomain adjacent to zinc finger domain protein 2A
C: Bromodomain adjacent to zinc finger domain protein 2A
D: Bromodomain adjacent to zinc finger domain protein 2A
E: ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
F: ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
G: ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,39719
Polymers29,4967
Non-polymers90012
Water3,189177
1
A: Bromodomain adjacent to zinc finger domain protein 2A
E: ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8595
Polymers7,6332
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8234
Polymers6,5981
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain adjacent to zinc finger domain protein 2A
G: ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8565
Polymers7,6332
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain adjacent to zinc finger domain protein 2A
F: ALA-ARG-THR-ALA-ALA-THR-ALA-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8595
Polymers7,6332
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.719, 72.719, 99.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 7 molecules ABCDEFG

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


Mass: 6597.694 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9
#2: Protein/peptide ALA-ARG-THR-ALA-ALA-THR-ALA-ARG


Mass: 1035.179 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 189 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2-2.4 M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→45.72 Å / Num. obs: 18751 / % possible obs: 99.9 % / Redundancy: 9.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementResolution: 2→45.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.917 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.15 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22255 955 5.1 %RANDOM
Rwork0.19381 ---
obs0.19525 17759 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.622 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å20 Å2
2--0.57 Å20 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 2→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 29 177 1934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191813
X-RAY DIFFRACTIONr_bond_other_d0.0020.021641
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9682438
X-RAY DIFFRACTIONr_angle_other_deg1.0573.0153757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1135226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75523.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.40915286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4691512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
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_it0.6852.831919
X-RAY DIFFRACTIONr_mcbond_other0.6852.827918
X-RAY DIFFRACTIONr_mcangle_it1.2434.2191137
X-RAY DIFFRACTIONr_mcangle_other1.2434.2231138
X-RAY DIFFRACTIONr_scbond_it0.5562.761894
X-RAY DIFFRACTIONr_scbond_other0.5562.764895
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9684.1621299
X-RAY DIFFRACTIONr_long_range_B_refined5.05733.5441920
X-RAY DIFFRACTIONr_long_range_B_other5.05533.571921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 71 -
Rwork0.225 1284 -
obs--99.85 %
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)
12.4198-1.39751.68352.2669-1.50012.63390.01640.1748-0.0967-0.2205-0.10040.00990.15740.17380.08390.08960.01680.0130.078-0.02010.034212.206933.266420.4187
22.1189-0.5048-1.23072.30960.79712.7895-0.0764-0.23570.0119-0.1137-0.1294-0.0569-0.04560.35570.20580.0255-0.0001-0.00010.11010.06580.085939.377125.417545.4111
30.71230.3035-0.85952.5087-1.27542.5775-0.01670.03690.00550.1104-0.03220.01940.08890.09660.04880.08850.0097-0.0040.04730.01170.058610.724339.146835.1042
42.4481.587-1.61521.3878-1.88513.0437-0.17560.1604-0.0381-0.12720.0473-0.07420.1778-0.00070.12830.0932-0.03060.04140.05110.03460.082633.690324.543230.7069
51.60871.3205-2.54611.4696-2.18044.05250.08970.01610.2173-0.29150.182-0.1292-0.0493-0.0509-0.27170.3837-0.08950.30220.2177-0.13420.274717.596634.620810.7601
67.87928.7905-0.56710.39560.92594.17-1.21890.7905-0.6697-1.2090.9002-0.64520.4918-0.0280.31880.313-0.07340.16670.1055-0.04480.090235.573418.917821.5111
70.0701-0.98250.577114.5534-8.47884.94620.00040.03250.03270.0209-0.1788-0.2769-0.0110.13920.17840.00920.0274-0.02070.3085-0.00310.130516.730638.013443.4478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1676 - 1923
2X-RAY DIFFRACTION2B1677 - 1924
3X-RAY DIFFRACTION3C1676 - 1940
4X-RAY DIFFRACTION4D1676 - 1932
5X-RAY DIFFRACTION5E1 - 8
6X-RAY DIFFRACTION6F1 - 8
7X-RAY DIFFRACTION7G1 - 7

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