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- PDB-5t8r: Crystal structure of human BAZ2A PHD zinc finger in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5t8r
TitleCrystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3 10-mer
Components
  • Bromodomain adjacent to zinc finger domain protein 2A
  • Histone H3.1
KeywordsTRANSCRIPTION / PHD zinc fingers / histone3 / complex
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 / Chromatin modifying enzymes / telomere organization ...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 / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / nuclear receptor binding / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / histone binding / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / nuclear speck / cadherin binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Histone H3.1 / Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAmato, A. / Gadd, M.S. / Bortoluzzi, A. / Ciulli, A.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains.
Authors: Bortoluzzi, A. / Amato, A. / Lucas, X. / Blank, M. / Ciulli, A.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
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

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: Histone H3.1
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,49717
Polymers28,6916
Non-polymers80511
Water1,72996
1
A: Bromodomain adjacent to zinc finger domain protein 2A
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9745
Polymers7,7482
Non-polymers2263
Water362
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8214
Polymers6,5981
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain adjacent to zinc finger domain protein 2A
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8794
Polymers7,7482
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Bromodomain adjacent to zinc finger domain protein 2A
C: Bromodomain adjacent to zinc finger domain protein 2A
G: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7949
Polymers14,3463
Non-polymers4496
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-17 kcal/mol
Surface area7290 Å2
MethodPISA
6
B: Bromodomain adjacent to zinc finger domain protein 2A
D: Bromodomain adjacent to zinc finger domain protein 2A
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7028
Polymers14,3463
Non-polymers3575
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-17 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.607, 72.607, 99.431
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEG

#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 / Fragment: PHD domain, UNP residues 1673-1728
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 Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1150.332 Da / Num. of mol.: 2 / Fragment: UNP residues 2-11 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 4 types, 107 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.: 2 / 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.: 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2 M Na/K phosphate / PH range: 8 - 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.4→45.62 Å / Num. obs: 10901 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.495.80.7820.7181100
8.98-45.624.50.0570.999195.7

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qf2

4qf2


Resolution: 2.4→45.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.647 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.245
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 556 5.1 %RANDOM
Rwork0.1851 ---
obs0.1877 10309 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 500 Å2 / Biso mean: 52.134 Å2 / Biso min: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2--0.58 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2.4→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 24 96 1860
Biso mean--67.47 54.85 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191815
X-RAY DIFFRACTIONr_bond_other_d0.0020.021663
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9652438
X-RAY DIFFRACTIONr_angle_other_deg1.1233.0153793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66323.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33315294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2991513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02401
X-RAY DIFFRACTIONr_mcbond_it1.6093.9902
X-RAY DIFFRACTIONr_mcbond_other1.6083.895901
X-RAY DIFFRACTIONr_mcangle_it2.845.8131117
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 29 -
Rwork0.25 769 -
all-798 -
obs--99.87 %
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)
15.4857-2.90792.61196.5291-1.81825.52750.15460.3396-0.1716-0.3067-0.2212-0.11340.27710.47850.06660.05070.04250.01840.1140.00170.020512.75932.90319.719
25.3121-0.5201-0.81225.78780.31716.8676-0.0987-0.53230.15460.1420.0829-0.46370.2110.42470.01580.01030.0203-0.01160.0709-0.01490.040139.36524.66145.514
32.30231.5041-1.06366.5595-2.136.0671-0.0126-0.1642-0.00580.20820.0569-0.28710.12190.3274-0.04440.01730.0244-0.01160.0509-0.00690.020611.39238.67634.563
45.74332.3675-3.40964.8077-5.36478.7142-0.26730.33460.0695-0.49560.0795-0.28080.39990.06040.18790.1211-0.03550.05590.0391-0.00250.03933.74823.54230.213
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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