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- PDB-4v2v: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (2... -

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Basic information

Entry
Database: PDB / ID: 4v2v
TitleJMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (25-29) ARK(me3)SA
Components
  • HISTONE H3.1T
  • LYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / NON-HEME / IRON / 2-OXOGLUTARATE / DIOXYGENASE / OXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / 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 H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / 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 H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / 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 / positive regulation of neuron differentiation / Meiotic synapsis / methylated histone binding / 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 / Meiotic recombination / fibrillar center / 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 / extracellular exosome / 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. / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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: 2 Å
AuthorsChowdhury, R. / Madden, S.K. / 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 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Mar 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 1.4Jan 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.pdbx_ptnr1_label_alt_id / _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
D: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,38211
Polymers89,8044
Non-polymers5787
Water8,449469
1
B: LYSINE-SPECIFIC DEMETHYLASE 4A
D: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1735
Polymers44,9022
Non-polymers2713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-16.9 kcal/mol
Surface area15410 Å2
MethodPISA
2
A: LYSINE-SPECIFIC DEMETHYLASE 4A
C: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2096
Polymers44,9022
Non-polymers3074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-23.9 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.020, 149.910, 57.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-322-

ARG

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 4A / 1.14.11.- / JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JUMONJI DOMAIN-CONTAINING PROTEIN 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, 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 / H3/T / H3T / H3/G


Mass: 575.702 Da / Num. of mol.: 2 / Fragment: HISTONE H3K27ME3 PEPTIDE, RESIDUES 25-29 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16695

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Non-polymers , 5 types, 476 molecules

#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 469 / 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 (1:1), 277 K, JCSG/A9: 0.2 M AMMONIUM CHLORIDE, 20 % W/V PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2014 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2→53.59 Å / Num. obs: 59803 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 34.18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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 ENTRY 2OX0

2ox0


Resolution: 2→53.589 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 3018 5.1 %
Rwork0.186 --
obs0.1877 59736 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→53.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 25 469 6170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086109
X-RAY DIFFRACTIONf_angle_d1.188325
X-RAY DIFFRACTIONf_dihedral_angle_d14.9782226
X-RAY DIFFRACTIONf_chiral_restr0.052854
X-RAY DIFFRACTIONf_plane_restr0.0071087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.03130.34111530.29352534X-RAY DIFFRACTION100
2.0313-2.06460.30641450.29292530X-RAY DIFFRACTION100
2.0646-2.10020.28741250.26412549X-RAY DIFFRACTION100
2.1002-2.13840.27641200.25582543X-RAY DIFFRACTION100
2.1384-2.17950.27251280.24552540X-RAY DIFFRACTION100
2.1795-2.2240.30421360.24272548X-RAY DIFFRACTION100
2.224-2.27230.25561420.22752550X-RAY DIFFRACTION100
2.2723-2.32520.23961350.22832549X-RAY DIFFRACTION100
2.3252-2.38330.26921150.22072590X-RAY DIFFRACTION100
2.3833-2.44780.26951720.2132478X-RAY DIFFRACTION100
2.4478-2.51980.25451350.20742595X-RAY DIFFRACTION100
2.5198-2.60110.25251510.21252537X-RAY DIFFRACTION100
2.6011-2.69410.31151300.21242554X-RAY DIFFRACTION100
2.6941-2.8020.25061420.19932562X-RAY DIFFRACTION100
2.802-2.92950.21961250.20532582X-RAY DIFFRACTION100
2.9295-3.08390.25231250.19082608X-RAY DIFFRACTION100
3.0839-3.27710.23061390.1842576X-RAY DIFFRACTION100
3.2771-3.53010.23611470.16922576X-RAY DIFFRACTION100
3.5301-3.88520.19131370.16652624X-RAY DIFFRACTION100
3.8852-4.44720.15961380.14792634X-RAY DIFFRACTION100
4.4472-5.60210.16531490.1332645X-RAY DIFFRACTION100
5.6021-53.60780.18841290.17622814X-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)
12.0665-1.3534-1.06743.6631-0.05382.40820.45930.3940.5156-0.6479-0.3217-1.2211-0.49570.3289-0.06040.50570.0550.21650.45980.1650.5574-5.7053-46.0984-28.8909
21.30370.19850.66251.4569-0.23070.71290.47010.9014-0.3174-0.9909-0.7630.4674-0.351-0.74910.27210.57140.2281-0.18280.6482-0.24480.3003-28.0034-53.2481-30.488
31.95580.1202-0.49171.3372-0.02771.22620.3560.951-0.3105-0.7684-0.63890.54-0.1985-0.55360.05190.39370.2174-0.24620.6276-0.22780.3134-29.2016-54.1036-28.6332
42.5612-1.3742-0.76152.98681.03311.31560.19050.1776-0.1141-0.1627-0.3196-0.0301-0.0647-0.13070.08230.19890.0105-0.0370.27370.01210.2178-19.7287-52.3402-17.9928
52.0246-1.11340.87713.17360.55110.96280.06430.15880.46830.0896-0.0735-0.7401-0.45940.7074-0.06790.39040.01580.01320.52960.06650.62481.1223-58.1617-13.8483
63.994-1.4996-0.10521.11960.95821.73510.08490.149-0.2975-0.8017-0.11810.712-0.3414-0.47890.0460.59020.033-0.13080.3293-0.00030.4151-25.9313-21.6839-8.3771
72.12460.08740.6821.58780.77141.58010.01940.3692-0.078-0.87430.2034-0.2268-0.56650.4109-0.07340.6776-0.19130.18950.3404-0.04870.2534-8.1253-18.2782-5.9742
81.71870.11060.30411.0048-0.25590.74490.07590.18110.0213-0.50290.434-0.7975-0.29910.79020.01780.4457-0.21740.31190.5442-0.21580.54274.7313-26.0979-0.5421
91.8587-0.1733-0.01232.40130.7692.32470.0215-0.10560.0452-0.40140.2013-0.0846-0.45070.2407-0.13860.3452-0.11480.1050.2083-0.03710.2361-10.4114-20.37443.4485
102.4727-1.8465-1.21932.26460.10481.0286-0.0442-0.0125-0.0341-0.24650.02480.3831-0.057-0.11020.00880.3461-0.0108-0.01340.3321-0.02740.4285-27.8254-13.034312.5888
111.28070.8523-0.71220.6465-0.87092.2004-0.1269-0.6816-0.21810.20580.00310.39680.052-0.29450.00430.55630.1003-0.08440.6582-0.0820.8566-25.5873-63.1576-18.8868
122.0551.39521.34181.49080.07792.1441-0.0937-0.2343-0.06190.167-0.1004-0.1568-0.1633-0.00510.00920.774-0.19650.08780.8348-0.10710.6728-7.0297-11.00618.2651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 42 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 43 THROUGH 82 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 83 THROUGH 162 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 163 THROUGH 322 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 323 THROUGH 355 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 7 THROUGH 36 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 37 THROUGH 78 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 79 THROUGH 124 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 125 THROUGH 293 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 294 THROUGH 354 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 25 THROUGH 29 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 25 THROUGH 29 )

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