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- PDB-8wd3: The Crystal Structure of JMJD2A(M1-L359) from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8wd3
TitleThe Crystal Structure of JMJD2A(M1-L359) from Biortus.
ComponentsLysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / Chromatin regulator Dioxygenase Oxidoreductase Transcription
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 / positive regulation of gene expression / chromatin / 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
NICKEL (II) ION / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of JMJD2A(M1-L359) from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Shang, H.
History
DepositionSep 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)88,9016
Polymers88,6532
Non-polymers2484
Water724
1
A: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4503
Polymers44,3261
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4503
Polymers44,3261
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.641, 97.111, 141.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Lysine-specific demethylase 4A


Mass: 44326.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A / Production host: Escherichia coli (E. coli) / References: UniProt: O75164
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M KSCN, 0.1M Bis-Tris propane pH7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18057 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18057 Å / Relative weight: 1
ReflectionResolution: 3.3→48.603 Å / Num. obs: 11222 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.162 / Net I/σ(I): 6.9
Reflection shellResolution: 3.3→3.56 Å / Rmerge(I) obs: 0.675 / Num. unique obs: 2264 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.603 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 109.738 / SU ML: 0.776 / Cross valid method: FREE R-VALUE / ESU R Free: 0.709
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2928 560 5.004 %
Rwork0.2439 10630 -
all0.246 --
obs-11190 99.608 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 96.393 Å2
Baniso -1Baniso -2Baniso -3
1-10.332 Å2-0 Å20 Å2
2---6.986 Å2-0 Å2
3----3.346 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5482 0 4 4 5490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165107
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.6767729
X-RAY DIFFRACTIONr_angle_other_deg0.3361.57811761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.843530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96210856
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.67910269
X-RAY DIFFRACTIONr_chiral_restr0.0440.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021398
X-RAY DIFFRACTIONr_nbd_refined0.2190.21208
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.25028
X-RAY DIFFRACTIONr_nbtor_refined0.1890.22812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3140.220
X-RAY DIFFRACTIONr_nbd_other0.2490.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.050.22
X-RAY DIFFRACTIONr_mcbond_it3.955.8142735
X-RAY DIFFRACTIONr_mcbond_other3.9495.8142735
X-RAY DIFFRACTIONr_mcangle_it6.51810.4453412
X-RAY DIFFRACTIONr_mcangle_other6.51810.4453413
X-RAY DIFFRACTIONr_scbond_it3.7265.9632958
X-RAY DIFFRACTIONr_scbond_other3.7255.9642959
X-RAY DIFFRACTIONr_scangle_it5.89810.8744313
X-RAY DIFFRACTIONr_scangle_other5.89810.8744314
X-RAY DIFFRACTIONr_lrange_it11.77170.07123974
X-RAY DIFFRACTIONr_lrange_other11.77170.07123975
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.3-3.3850.309400.3677640.3658040.880.8881000.349
3.385-3.4780.318350.3527560.357920.8920.89499.87370.321
3.478-3.5780.346470.3197200.3217680.9070.91799.86980.298
3.578-3.6880.348350.3147170.3167540.9290.92599.73470.291
3.688-3.8080.305380.276760.2727170.9320.94699.58160.242
3.808-3.940.343320.2666760.2697100.8920.9599.71830.248
3.94-4.0880.262300.2446310.2456700.9550.95698.65670.229
4.088-4.2540.205360.2396220.2376590.9720.95799.84830.221
4.254-4.4410.343320.2235940.2296260.9220.9651000.209
4.441-4.6560.293340.2015640.2066000.9430.9799.66670.192
4.656-4.9060.265320.2145500.2175820.9520.9681000.207
4.906-5.20.357360.1945140.2045560.9150.97698.92090.187
5.2-5.5540.217230.2044850.2055110.9710.97399.41290.196
5.554-5.9930.304190.2164640.224840.9550.96999.79340.212
5.993-6.5550.286290.2144330.2194620.9550.9681000.209
6.555-7.3120.334140.2333930.2374070.9260.9641000.231
7.312-8.4120.247160.1993530.2013730.9450.97498.92760.205
8.412-10.2260.217140.23050.2013210.980.97999.37690.214
10.226-14.1520.284110.2052500.2092630.9690.97599.23950.219
14.152-48.6030.35370.3541630.3541710.9720.92999.41520.393
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)
13.0235-0.5253-0.77966.39182.34774.21590.03150.18690.1993-0.73530.3422-0.439-0.126-0.0172-0.37380.093-0.04350.0090.0392-0.03820.506120.88939.00118.466
23.9157-0.1994-0.17254.1847-0.70151.34050.0874-0.4126-0.370.2955-0.1223-0.0025-0.58110.26420.03490.2556-0.11780.02390.09010.01970.4743-3.93634.37151.794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA9 - 355
2X-RAY DIFFRACTION2B7 - 353

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