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- PDB-7eqv: Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 7eqv
TitleCrystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / Human histone lysine demethylase 4A / Lysine-specific demethylase 4A / KDM4A / JMJD2A / 3 / 4-dihydroxybenzoic acid / Inhibitor
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / pericentric heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain ...: / : / : / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / PHD-finger / PHD-zinc-finger like domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
3,4-DIHYDROXYBENZOIC ACID / NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsFang, W.-K. / Yang, S.-M. / Wang, W.-C.
CitationJournal: J.Biomed.Sci. / Year: 2022
Title: Natural product myricetin is a pan-KDM4 inhibitor which with poly lactic-co-glycolic acid formulation effectively targets castration-resistant prostate cancer.
Authors: Liu, J.S. / Fang, W.K. / Yang, S.M. / Wu, M.C. / Chen, T.J. / Chen, C.M. / Lin, T.Y. / Liu, K.L. / Wu, C.M. / Chen, Y.C. / Chuu, C.P. / Wang, L.Y. / Hsieh, H.P. / Kung, H.J. / Wang, W.C.
History
DepositionMay 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8875
Polymers40,5731
Non-polymers3144
Water2,702150
1
A: Lysine-specific demethylase 4A
hetero molecules

A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,77410
Polymers81,1472
Non-polymers6278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1260 Å2
ΔGint-29 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.396, 149.396, 62.175
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-611-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4A / JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / ...JmjC domain-containing histone demethylation protein 3A / Jumonji domain-containing protein 2A / [histone H3]-trimethyl-L-lysine(36) demethylase 4A / [histone H3]-trimethyl-L-lysine(9) demethylase 4A


Mass: 40573.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Production host: Escherichia coli (E. coli)
References: UniProt: O75164, [histone H3]-trimethyl-L-lysine9 demethylase, [histone H3]-trimethyl-L-lysine36 demethylase

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Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-DHB / 3,4-DIHYDROXYBENZOIC ACID / Protocatechuic acid


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.94 Å3/Da / Density % sol: 75.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.1 M HEPES pH 7.5, 0.2M NaCl, 277 K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2018
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.6→129.38 Å / Num. obs: 24683 / % possible obs: 99.6 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.017 / Rrim(I) all: 0.072 / Χ2: 0.976 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.69120.68723520.9080.1920.7160.87996.1
2.69-2.8160.62424520.9690.1590.6450.89199.9
2.8-2.9318.70.48624480.9840.1150.4990.896100
2.93-3.0819.20.27424580.9950.0640.2820.927100
3.08-3.2819.20.1724540.9970.040.1750.951100
3.28-3.5319.20.11224710.9990.0260.1150.989100
3.53-3.88190.07424770.9990.0180.0771.004100
3.88-4.4418.80.05524890.9990.0130.0561.071100
4.44-5.5918.30.05125020.9990.0120.0531.371100
5.59-3017.30.03258010.0070.0310.72399.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å29.68 Å
Translation2.6 Å29.68 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BIS

4bis


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.041 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1112 4.9 %RANDOM
Rwork0.1681 ---
obs0.1706 21751 92.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.29 Å2 / Biso mean: 43.64 Å2 / Biso min: 3.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 14 150 2963
Biso mean--76.14 36.75 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192895
X-RAY DIFFRACTIONr_bond_other_d0.0010.022621
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.9473918
X-RAY DIFFRACTIONr_angle_other_deg0.94836086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2225339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49323.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52715492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1611519
X-RAY DIFFRACTIONr_chiral_restr0.1090.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
LS refinement shellResolution: 2.602→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 50 -
Rwork0.253 813 -
all-863 -
obs--47.97 %

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