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- PDB-4v2w: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) -

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Basic information

Entry
Database: PDB / ID: 4v2w
TitleJMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35)
Components
  • HISTONE H3.1T
  • LYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / JMJD2A / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / DEMETHYLASE / HISTONE / JMJC DOMAIN / METAL BINDING PROTEIN / EPIGENETIC AND TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / HYDROXYLATION
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 / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / methylated histone binding / Meiotic synapsis / positive regulation of neuron differentiation / negative regulation of autophagy / response to nutrient levels / Condensation of Prophase Chromosomes / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / Meiotic recombination / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Processing of DNA double-strand break ends / regulation of gene expression / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / DNA binding / zinc ion binding / extracellular exosome / 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. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4A / Histone H3.1t
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsChowdhury, R. / Zafred, D. / Schofield, C.J.
CitationJournal: Epigenetics / Year: 2014
Title: Studies on the Catalytic Domains of Multiple Jmjc Oxygenases Using Peptide Substrates.
Authors: Williams, S.T. / Walport, L.J. / Hopkinson, R.J. / Madden, S.K. / Chowdhury, R. / Schofield, C.J. / Kawamura, A.
History
DepositionOct 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Feb 11, 2015Group: Database references
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_auth_atom_name / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,41312
Polymers90,7083
Non-polymers7059
Water9,008500
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
C: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7807
Polymers46,3822
Non-polymers3995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-26.3 kcal/mol
Surface area15470 Å2
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6335
Polymers44,3261
Non-polymers3074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.711, 149.740, 57.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 4A / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JUMONJI DOMAIN-CONTAINING PROTEIN 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN 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) / Variant (production host): R3
References: UniProt: O75164, 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
#2: Protein/peptide HISTONE H3.1T


Mass: 2055.447 Da / Num. of mol.: 1 / Fragment: HISTONE H3K27ME3 PEPTIDE, RESIDUES 17-36 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q16695

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Non-polymers , 6 types, 509 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.64 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: VAPOUR DIFFUSION, SITTING DROP (PROTEIN:WELL, 1:2), 277 K, PACT PREMIER/G10: 0.02 M SODIUM/POTASSIUM PHOSPHATE, 0.1 M BIS TRIS PROPANE 7.5, 20 % W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.81→60.07 Å / Num. obs: 79999 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 31.89 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.9
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENRTY 2OX0

2ox0


Resolution: 1.81→60.072 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 4010 5 %
Rwork0.1724 --
obs0.1742 79914 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→60.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5646 0 32 500 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016182
X-RAY DIFFRACTIONf_angle_d1.3218436
X-RAY DIFFRACTIONf_dihedral_angle_d14.962273
X-RAY DIFFRACTIONf_chiral_restr0.058863
X-RAY DIFFRACTIONf_plane_restr0.0081110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.83130.34911370.30772485X-RAY DIFFRACTION97
1.8313-1.85360.33711240.29592613X-RAY DIFFRACTION99
1.8536-1.87710.26361220.27952587X-RAY DIFFRACTION100
1.8771-1.90180.31331340.27382592X-RAY DIFFRACTION100
1.9018-1.92790.27961340.26392588X-RAY DIFFRACTION100
1.9279-1.95540.30831370.25032565X-RAY DIFFRACTION100
1.9554-1.98460.24391420.23862624X-RAY DIFFRACTION100
1.9846-2.01560.271430.22892562X-RAY DIFFRACTION100
2.0156-2.04870.27761500.23192574X-RAY DIFFRACTION100
2.0487-2.0840.25731480.23162576X-RAY DIFFRACTION100
2.084-2.12190.26381400.21972616X-RAY DIFFRACTION100
2.1219-2.16270.23521300.20992584X-RAY DIFFRACTION100
2.1627-2.20680.2391520.21252611X-RAY DIFFRACTION100
2.2068-2.25480.23131430.20112559X-RAY DIFFRACTION100
2.2548-2.30730.20461550.19662617X-RAY DIFFRACTION100
2.3073-2.3650.23131230.19042599X-RAY DIFFRACTION100
2.365-2.42890.20721310.18672627X-RAY DIFFRACTION100
2.4289-2.50040.21791430.18562615X-RAY DIFFRACTION100
2.5004-2.58110.22541420.19152610X-RAY DIFFRACTION100
2.5811-2.67340.221360.19712599X-RAY DIFFRACTION100
2.6734-2.78040.21841400.17872633X-RAY DIFFRACTION100
2.7804-2.90690.21661310.1892624X-RAY DIFFRACTION100
2.9069-3.06020.23931300.17692656X-RAY DIFFRACTION100
3.0602-3.25190.19621440.17182618X-RAY DIFFRACTION100
3.2519-3.5030.19171360.15912652X-RAY DIFFRACTION100
3.503-3.85540.19971240.14932695X-RAY DIFFRACTION100
3.8554-4.41320.16781340.12932684X-RAY DIFFRACTION100
4.4132-5.55950.16631530.12052698X-RAY DIFFRACTION100
5.5595-60.10510.18571520.15352841X-RAY DIFFRACTION100
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)
15.7582.9779-2.53392.2119-0.16713.5360.1523-0.18760.34240.3385-0.14971.14250.5286-0.53910.00550.5751-0.02440.11010.3431-0.04110.5257-24.430823.3652-18.9326
22.69420.2046-0.48522.69140.60282.95040.0126-0.113-0.01340.51530.2031-0.09260.54590.3953-0.10880.36730.1425-0.12210.1956-0.04040.2166-7.850420.8546-29.6755
32.76652.14371.07873.2280.75182.177-0.04340.0335-0.11350.1465-0.01470.29980.1391-0.1790.05740.3438-0.0091-0.02840.3034-0.01290.4932-27.732312.8837-41.4742
40.98610.7225-0.66123.43060.86633.63920.3951-0.6688-0.4140.8447-0.0178-1.27110.37050.8493-0.36120.5668-0.0903-0.28350.61030.16040.6379-6.65144.83732.1044
52.3350.88260.65112.37090.26141.29210.4869-1.07050.05630.7182-0.58840.32620.2381-0.55870.18780.3983-0.16780.16970.6767-0.16120.255-28.778551.1126-0.3054
63.01871.1280.58953.18270.58961.38640.2352-0.51450.10580.3134-0.3718-0.06660.0787-0.28270.10810.2183-0.03830.02640.30340.0090.1647-19.183154.6679-6.2624
73.08191.22280.6473.30331.21070.89990.2403-0.2062-0.14530.1711-0.3226-0.05440.1092-0.20820.06230.207-0.02420.03380.26330.02370.2057-22.688946.2929-11.9027
82.90182.09590.33123.34680.55513.3443-0.04690.08870.2281-0.15110.0012-0.2236-0.27350.0921-0.04030.20330.00450.01550.23440.0260.3042-8.675662.2986-14.4125
91.61291.627-1.71235.34170.24343.44260.0414-0.104-0.44450.1739-0.202-0.820.26040.81990.26090.32560.0427-0.00230.49020.0540.7611.075752.9636-11.1312
108.8506-8.1815-6.17238.68835.79024.31130.01930.1656-0.0372-0.373-0.11010.06630.1622-0.1008-0.0071.2305-0.2218-0.27661.18260.10011.3514-8.027710.2493-36.8582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 7 THROUGH 26 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 27 THROUGH 293 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 294 THROUGH 354 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 3 THROUGH 26 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 27 THROUGH 144 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 145 THROUGH 226 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 227 THROUGH 283 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 284 THROUGH 333 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 334 THROUGH 355 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 25 THROUGH 28 )

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