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- PDB-6fap: Crystal structure of human BAZ2A PHD zinc finger in complex with Fr23 -

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Basic information

Entry
Database: PDB / ID: 6fap
TitleCrystal structure of human BAZ2A PHD zinc finger in complex with Fr23
ComponentsBromodomain adjacent to zinc finger domain protein 2A
KeywordsTRANSCRIPTION
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 / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
~{N}-(4-aminophenyl)-2-azanyl-ethanamide / PHOSPHATE ION / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionDec 16, 2017Deposition 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 1.3Jan 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

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,62118
Polymers26,3914
Non-polymers1,23114
Water46826
1
A: 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
2
B: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9895
Polymers6,5981
Non-polymers3914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain adjacent to zinc finger domain protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9865
Polymers6,5981
Non-polymers3884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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
Unit cell
Length a, b, c (Å)72.796, 72.796, 99.630
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 , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 40 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-D3H / ~{N}-(4-aminophenyl)-2-azanyl-ethanamide


Mass: 165.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O
#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.: 26 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4 M sodium/ potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.7→45.73 Å / Num. obs: 7841 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 995 / CC1/2: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qf2

4qf2


Resolution: 2.7→45.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.772 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.881 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24798 401 5.1 %RANDOM
Rwork0.20884 ---
obs0.21078 7407 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.721 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å2-0 Å2-0 Å2
2--1.87 Å20 Å2
3----3.73 Å2
Refinement stepCycle: 1 / Resolution: 2.7→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1595 0 53 26 1674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191700
X-RAY DIFFRACTIONr_bond_other_d0.0010.021495
X-RAY DIFFRACTIONr_angle_refined_deg0.7461.9852286
X-RAY DIFFRACTIONr_angle_other_deg0.6413.0223428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50423.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98915263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3131510
X-RAY DIFFRACTIONr_chiral_restr0.050.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021843
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
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_it1.1914.763832
X-RAY DIFFRACTIONr_mcbond_other1.194.762831
X-RAY DIFFRACTIONr_mcangle_it2.0117.1351033
X-RAY DIFFRACTIONr_mcangle_other2.0117.1351034
X-RAY DIFFRACTIONr_scbond_it1.6894.995868
X-RAY DIFFRACTIONr_scbond_other1.6884.999869
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2947.4281254
X-RAY DIFFRACTIONr_long_range_B_refined3.61254.3721714
X-RAY DIFFRACTIONr_long_range_B_other3.61254.3651714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 28 -
Rwork0.265 524 -
obs--100 %
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)
16.0335-2.70884.18595.7783-1.88617.11870.26070.5026-0.3228-0.5265-0.273-0.0920.41330.50030.01220.08210.01730.03780.09290.00080.086812.758832.903519.7191
26.13680.8227-1.87467.93211.27446.7779-0.1631-0.2673-0.1468-0.07780.0396-0.54160.16930.60870.12350.03240.00950.02360.08480.04360.086639.36524.661445.5144
34.52240.0882-1.82486.9887-1.39775.60590.0042-0.08380.10420.1783-0.1918-0.14430.08130.23760.18760.03630.0158-0.01280.03880.02890.067511.392238.675834.5627
45.95613.8444-2.18765.6756-3.54196.9309-0.26220.3969-0.3532-0.5330.0333-0.27620.44580.20050.22880.09470.01050.07410.0544-0.01340.100733.747823.541830.2127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1676 - 1728
2X-RAY DIFFRACTION2B1676 - 1726
3X-RAY DIFFRACTION3C1676 - 1727
4X-RAY DIFFRACTION4D1676 - 1728

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