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- PDB-2wwj: STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A -

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Basic information

Entry
Database: PDB / ID: 2wwj
TitleSTRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A
ComponentsLYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE / CHROMATIN REGULATOR / DOUBLE-STRANDED BETA HELIX / TRANSCRIPTION / OXYGENASE / HOST-VIRUS INTERACTION / TRANSCRIPTION REGULATION
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 / response to nutrient levels / negative regulation of autophagy / 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. / Cupin / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / O-benzyl-N-(carboxycarbonyl)-D-tyrosine / Lysine-specific demethylase 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRose, N.R. / Clifton, I.J. / Oppermann, U. / McDonough, M.A. / Schofield, C.J.
CitationJournal: J. Med. Chem. / Year: 2010
Title: Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches.
Authors: Rose, N.R. / Woon, E.C. / Kingham, G.L. / King, O.N. / Mecinovic, J. / Clifton, I.J. / Ng, S.S. / Talib-Hardy, J. / Oppermann, U. / McDonough, M.A. / Schofield, C.J.
History
DepositionOct 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 20, 2023Group: 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_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.pdbx_dist_value / _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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0018
Polymers81,0662
Non-polymers9356
Water2,594144
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0014
Polymers40,5331
Non-polymers4673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0014
Polymers40,5331
Non-polymers4673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.330, 148.970, 57.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998847, 0.034129, 0.033748), (-0.029647, -0.991664, 0.125396), (0.037746, 0.124251, 0.991533)
Vector: -67.168, -77.686, -16.896)

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Components

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


Mass: 40533.199 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC28BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O75164, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-Y28 / O-benzyl-N-(carboxycarbonyl)-D-tyrosine / (2R)-2-(carboxycarbonylamino)-3-(4-phenylmethoxyphenyl)propanoic acid


Type: D-peptide linking / Mass: 343.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17NO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN STOCK 11MG/ML JMJD2A, 10MM HEPES PH7.5, 500MM NACL, 5% GLYCEROL, 0.75MM INHIBITOR 10A. RESERVOIR: 0.1M CITRATE PH5.5, 18.5% PEG3350, 4MM NICL2. 1:1 PROTEIN/RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.6→49.75 Å / Num. obs: 27338 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.64 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.37 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OQ6

2oq6


Resolution: 2.6→47.97 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.891 / SU B: 21.504 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.24758 1191 4.4 %RANDOM
Rwork0.17799 ---
obs0.18104 26102 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 54 144 5895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225944
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9528036
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.695695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14323.171287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48615999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5241539
X-RAY DIFFRACTIONr_chiral_restr0.1060.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.51504
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48922435
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.56131049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0974.51022
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 73 -
Rwork0.241 1874 -
obs--99.39 %
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)
13.0158-0.6387-0.13862.05630.84572.80230.03850.3056-0.0432-0.30070.00590.17090.0493-0.1784-0.04430.07090.0052-0.04650.1225-0.0430.1295-42.184-26.463-32.584
20.9907-0.03070.17261.4762-0.96491.79790.04450.34150.0166-0.278-0.0896-0.1140.02660.18460.0450.07850.01760.03850.14110.00930.0971-14.373-23.422-27.792
31.4109-0.3637-0.07861.03820.11870.74670.01720.08190.0477-0.0685-0.02450.0156-0.0348-0.01140.00720.0308-0.0145-0.00870.0561-0.01040.0451-29.324-22.324-21.401
411.564915.9647035.661109.51750.38151.22751.5759-0.970.3229-0.4528-0.3055-0.5784-0.70451.5132-0.23420.42050.91030.4770.7353-24.658-11.245-6.473
511.18522.6074-0.79862.67211.05784.944-0.1903-0.41390.47290.17090.0963-0.0336-0.2243-0.07290.09410.17660.0263-0.01790.101-0.0330.1267-41.326-7.624-12.942
61.3655-0.7946-0.9954.83751.07761.6132-0.0613-0.0826-0.11610.1535-0.01730.21820.1047-0.17590.07870.0225-0.00060.01060.13990.01160.1573-51.383-16.213-13.385
71.44950.2476-0.25710.98970.13391.1263-0.05330.245-0.1589-0.18580.0247-0.01060.1196-0.0840.02850.10430.0013-0.01660.08080.010.0788-42.249-54.504-4.733
83.6289-1.3974-1.36473.24040.9021.80230.1260.27290.0228-0.3665-0.12170.0281-0.0629-0.0881-0.00440.1303-0.0339-0.05960.18480.0240.0614-46.85-52.516-4.158
916.07085.1037-6.868115.7009-1.98828.2728-0.08730.28-1.5236-0.5834-0.0934-0.20421.69910.04270.18060.58450.0652-0.17570.0453-0.04290.2087-27.753-71.4662.746
102.6417-0.34451.13330.91590.19382.42260.0074-0.0896-0.21890.06220.0211-0.04260.23680.0936-0.02840.0566-0.00920.01670.05550.01340.0555-40.096-54.8672.738
118.42582.0761-1.472720.2434-6.414415.30840.152-0.413-0.10660.428-0.2153-0.6147-0.27290.67970.06330.03110.0035-0.02560.0932-0.03140.0453-41.75-46.56922.183
120.97590.03180.18440.9158-0.01241.26940.0055-0.067-0.01490.02690.0108-0.07340.03980.0399-0.01640.0575-0.01370.00310.0750.00510.0875-37.206-50.9065.207
132.71913.9785-0.432110.6033-5.36244.80380.00420.8025-1.1467-1.20130.6552-0.68841.31050.4239-0.65930.89050.0754-0.01320.3985-0.37440.979-43.896-63.54420.312
141.937-0.72381.02342.4082-0.77821.1793-0.0242-0.15-0.04070.1479-0.0437-0.22410.00440.13860.06780.0720.0141-0.00730.1025-0.01060.1388-20.086-62.09212.124
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 53
2X-RAY DIFFRACTION2A54 - 119
3X-RAY DIFFRACTION3A120 - 306
4X-RAY DIFFRACTION4A307 - 311
5X-RAY DIFFRACTION5A312 - 322
6X-RAY DIFFRACTION6A323 - 353
7X-RAY DIFFRACTION7B7 - 109
8X-RAY DIFFRACTION8B110 - 153
9X-RAY DIFFRACTION9B154 - 163
10X-RAY DIFFRACTION10B164 - 220
11X-RAY DIFFRACTION11B221 - 235
12X-RAY DIFFRACTION12B236 - 306
13X-RAY DIFFRACTION13B307 - 311
14X-RAY DIFFRACTION14B312 - 353

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