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- PDB-5a7s: Crystal structure of human JMJD2A in complex with compound 44 -

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Basic information

Entry
Database: PDB / ID: 5a7s
TitleCrystal structure of human JMJD2A in complex with compound 44
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A
Function / homology
Function and homology information


histone H3-tri/dimethyl-lysine-36 demethylase activity / [histone H3]-trimethyl-L-lysine36 demethylase / histone demethylation / histone H3-K36 demethylation / histone H3-methyl-lysine-36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3-tri/dimethyl-lysine-9 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / histone H3-K9 demethylation ...histone H3-tri/dimethyl-lysine-36 demethylase activity / [histone H3]-trimethyl-L-lysine36 demethylase / histone demethylation / histone H3-K36 demethylation / histone H3-methyl-lysine-36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3-tri/dimethyl-lysine-9 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / histone H3-K9 demethylation / histone H3-methyl-lysine-9 demethylase activity / negative regulation of astrocyte differentiation / pericentric heterochromatin / histone demethylase activity / negative regulation of cell death / negative regulation of autophagy / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / methylated histone binding / positive regulation of neuron differentiation / response to nutrient levels / HDMs demethylate histones / fibrillar center / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin remodeling / negative regulation of gene expression / negative regulation of transcription, DNA-templated / ubiquitin protein ligase binding / positive regulation of gene expression / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Jumonji domain-containing protein 2A Tudor domain / Lysine-specific demethylase 4, Tudor domain / Tudor domain / Tudor domain / Small domain found in the jumonji family of transcription factors / JmjN domain / jmjN domain / JmjN domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...Jumonji domain-containing protein 2A Tudor domain / Lysine-specific demethylase 4, Tudor domain / Tudor domain / Tudor domain / Small domain found in the jumonji family of transcription factors / JmjN domain / jmjN domain / JmjN domain profile. / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain profile. / JmjC domain / PHD zinc finger / Zinc finger, PHD-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-S2X / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNowak, R. / Velupillai, S. / Krojer, T. / Gileadi, C. / Johansson, C. / Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. ...Nowak, R. / Velupillai, S. / Krojer, T. / Gileadi, C. / Johansson, C. / Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / Kopec, J. / Tallant, C. / Froese, S. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Shoichet, B.K. / Fujimori, D.G. / Oppermann, U.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors.
Authors: Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Krojer, T. / Velupillai, S. / Gileadi, C. / Nowak, R.P. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / ...Authors: Korczynska, M. / Le, D.D. / Younger, N. / Gregori-Puigjane, E. / Tumber, A. / Krojer, T. / Velupillai, S. / Gileadi, C. / Nowak, R.P. / Iwasa, E. / Pollock, S.B. / Ortiz Torres, I. / Oppermann, U. / Shoichet, B.K. / Fujimori, D.G.
History
DepositionJul 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSINE-SPECIFIC DEMETHYLASE 4A
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,52525
Polymers88,6532
Non-polymers1,87223
Water7,098394
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,23112
Polymers44,3261
Non-polymers90511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,29413
Polymers44,3261
Non-polymers96712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.070, 100.760, 149.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#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 / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JUMONJI DOMAIN-CONTAINING PROTEIN 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one ...References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Non-polymers , 6 types, 417 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-S2X / 2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid


Mass: 272.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O4
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.66 Å3/Da / Density % sol: 2.66 % / Description: NONE
Crystal growpH: 8.5
Details: 30% PEG3350 -- 0.1M TRIS PH 8.5 -- 0.25M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97964
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 2.2→32.76 Å / Num. obs: 43913 / % possible obs: 98.8 % / Observed criterion σ(I): 2.8 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQ7
Resolution: 2.2→31.1935 Å / σ(F): 2 / Stereochemistry target values: ML
Details: DUAL CONFORMATION MODELED FOR SOME RESIDUES. SOME SIDE CHAINS ARE MISSING. DISORDERED REGIONS HAVE HIGH B FACTORS.
RfactorNum. reflection% reflection
Rfree0.2275 2125 4.8 %
Rwork0.1707 --
obs-41742 98.6995 %
Refinement stepCycle: LAST / Resolution: 2.2→31.1935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 112 394 6074

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