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- PDB-11af: Crystal structure of JADE3 PZP domain in complex with Histone H3 -

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Basic information

Entry
Database: PDB / ID: 11af
TitleCrystal structure of JADE3 PZP domain in complex with Histone H3
ComponentsHistone H3.1,Protein Jade-3
KeywordsTRANSCRIPTION / HBO1 / JADE / PZP / histone / DNA / chromatin
Function / homology
Function and homology information


regulation of DNA biosynthetic process / regulation of DNA replication / histone acetyltransferase complex / histone reader activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / epigenetic regulation of gene expression / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...regulation of DNA biosynthetic process / regulation of DNA replication / histone acetyltransferase complex / histone reader activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / epigenetic regulation of gene expression / 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 / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / 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) / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / HDMs demethylate histones / 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 / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / membrane / nucleus
Similarity search - Function
JADE3, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. ...JADE3, PHD domain / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / 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 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.1 / Protein Jade-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSelvam, K. / Gaurav, N. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)AG067664, CA252707, GM157928 United States
CitationJournal: Nat Commun / Year: 2026
Title: Distinct roles of the JADE and BRPF scaffolding subunits of the acetyltransferase HBO1 complex.
Authors: Gaurav, N. / Ebert, L.K. / Lachance, C. / Selvam, K. / Chen, R.W. / Qin, W. / Pozharskaia, V. / Chi, C. / Cote, V. / Cox, K.L. / Fuchs, H.A. / Musselman, C.A. / Leonhardt, H. / Morral, N. / ...Authors: Gaurav, N. / Ebert, L.K. / Lachance, C. / Selvam, K. / Chen, R.W. / Qin, W. / Pozharskaia, V. / Chi, C. / Cote, V. / Cox, K.L. / Fuchs, H.A. / Musselman, C.A. / Leonhardt, H. / Morral, N. / Song, K. / Poirier, M.G. / Cote, J. / Schermer, B. / Kutateladze, T.G.
History
DepositionFeb 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3.1,Protein Jade-3
B: Histone H3.1,Protein Jade-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,44312
Polymers41,7892
Non-polymers65410
Water97354
1
A: Histone H3.1,Protein Jade-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2216
Polymers20,8941
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone H3.1,Protein Jade-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2216
Polymers20,8941
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.887, 98.415, 104.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Histone H3.1,Protein Jade-3 / 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 / Jade family PHD finger protein 3 / PHD finger protein 16


Mass: 20894.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J, JADE3, KIAA0215, PHF16
Production host: Escherichia coli (E. coli) / References: UniProt: P68431, UniProt: Q92613
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 8.5 and 25% PEG 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.6→46.12 Å / Num. obs: 11979 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.957 / Rpim(I) all: 0.152 / Rrim(I) all: 0.373 / Χ2: 1.14 / Net I/σ(I): 5.7
Reflection shellResolution: 2.6→2.72 Å / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 1.046 / Num. measured all: 7967 / Num. unique obs: 1413 / CC1/2: 0.6 / Rpim(I) all: 0.484 / Rrim(I) all: 1.156 / Χ2: 0.91 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.59 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.862 / SU B: 13.078 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.181 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27762 612 5.2 %RANDOM
Rwork0.23189 ---
obs0.23422 11264 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.154 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å2-0 Å2
2--1.85 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 0 54 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162481
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.8133565
X-RAY DIFFRACTIONr_angle_other_deg0.6271.7635753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6185342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.985511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23410450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02540
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_it2.592.6141374
X-RAY DIFFRACTIONr_mcbond_other2.592.6141374
X-RAY DIFFRACTIONr_mcangle_it4.284.6781711
X-RAY DIFFRACTIONr_mcangle_other4.2794.681712
X-RAY DIFFRACTIONr_scbond_it2.6382.7451256
X-RAY DIFFRACTIONr_scbond_other2.6372.7481257
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2654.9721854
X-RAY DIFFRACTIONr_long_range_B_refined6.46623.532806
X-RAY DIFFRACTIONr_long_range_B_other6.45223.542803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 43 -
Rwork0.326 779 -
obs--98.68 %

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