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- PDB-6h8p: JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K... -

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Basic information

Entry
Database: PDB / ID: 6h8p
TitleJMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)
Components
  • Histone H1.4
  • Lysine-specific demethylase 4A
KeywordsOXIDOREDUCTASE / JMJD2A / KDM4A / 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 / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / cardiac muscle hypertrophy in response to stress / chromosome condensation / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / apoptotic chromosome condensation / histone H3K36 demethylase activity / negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / cardiac muscle hypertrophy in response to stress / chromosome condensation / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / nucleosomal DNA binding / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / histone H3K9 demethylase activity / negative regulation of astrocyte differentiation / histone demethylase activity / heterochromatin / 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 / euchromatin / HDMs demethylate histones / chromatin DNA binding / fibrillar center / histone deacetylase binding / nucleosome assembly / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of gene expression / double-stranded DNA binding / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / : / Linker histone H1/H5 / linker histone H1 and H5 family / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 ...: / : / : / Linker histone H1/H5 / linker histone H1 and H5 family / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4A / Histone H1.4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å
AuthorsChowdhury, R. / Walport, L.J. / Schofield, C.J.
Citation
Journal: FEBS Lett. / Year: 2018
Title: Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.
Authors: Walport, L.J. / Hopkinson, R.J. / Chowdhury, R. / Zhang, Y. / Bonnici, J. / Schiller, R. / Kawamura, A. / Schofield, C.J.
#1: Journal: Nature / Year: 2007
Title: Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / ...Authors: Ng, S.S. / Kavanagh, K.L. / McDonough, M.A. / Butler, D. / Pilka, E.S. / Lienard, B.M. / Bray, J.E. / Savitsky, P. / Gileadi, O. / von Delft, F. / Rose, N.R. / Offer, J. / Scheinost, J.C. / Borowski, T. / Sundstrom, M. / Schofield, C.J. / Oppermann, U.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.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

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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 H1.4
D: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,81216
Polymers91,8314
Non-polymers98212
Water8,179454
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A: Lysine-specific demethylase 4A
C: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4989
Polymers45,9152
Non-polymers5837
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-24 kcal/mol
Surface area15080 Å2
MethodPISA
2
B: Lysine-specific demethylase 4A
D: Histone H1.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3147
Polymers45,9152
Non-polymers3995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-26 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.722, 150.146, 57.601
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, 4 molecules ABCD

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 H1.4 / Histone H1b / Histone H1s-4


Mass: 1588.978 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10412

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Non-polymers , 6 types, 466 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 0.1 M MIB buffer (malonic acid/imidazole/boric acid, pH 6.0) 25% w/v polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.98→47.45 Å / Num. obs: 60704 / % possible obs: 99.1 % / Redundancy: 8.1 % / Biso Wilson estimate: 37.26 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.5
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.937 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5991 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OX0

2ox0


Resolution: 1.983→47.44 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 2968 4.9 %
Rwork0.192 --
obs0.193 60572 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 48.3 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 56 Å2
Refinement stepCycle: LAST / Resolution: 1.983→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5679 0 50 454 6183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055950
X-RAY DIFFRACTIONf_angle_d0.8868079
X-RAY DIFFRACTIONf_dihedral_angle_d15.5333488
X-RAY DIFFRACTIONf_chiral_restr0.049832
X-RAY DIFFRACTIONf_plane_restr0.0081043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9826-2.01510.30221330.31132459X-RAY DIFFRACTION90
2.0151-2.04990.32371470.30222718X-RAY DIFFRACTION100
2.0499-2.08710.32131430.28742721X-RAY DIFFRACTION99
2.0871-2.12730.27061180.27312772X-RAY DIFFRACTION99
2.1273-2.17070.28131410.25962694X-RAY DIFFRACTION100
2.1707-2.21790.30121330.26092767X-RAY DIFFRACTION100
2.2179-2.26950.28081320.25292731X-RAY DIFFRACTION100
2.2695-2.32620.28151740.25632734X-RAY DIFFRACTION100
2.3262-2.38910.27731300.23962756X-RAY DIFFRACTION99
2.3891-2.45940.2371410.23272735X-RAY DIFFRACTION99
2.4594-2.53880.27171580.2262726X-RAY DIFFRACTION100
2.5388-2.62950.25051390.23042786X-RAY DIFFRACTION100
2.6295-2.73480.25371410.2252567X-RAY DIFFRACTION93
2.7348-2.85930.27671320.22422762X-RAY DIFFRACTION99
2.8593-3.010.24321310.20682805X-RAY DIFFRACTION100
3.01-3.19850.20631410.18862774X-RAY DIFFRACTION100
3.1985-3.44540.19861370.17892811X-RAY DIFFRACTION100
3.4454-3.7920.16641330.16312816X-RAY DIFFRACTION100
3.792-4.34040.16391590.14632811X-RAY DIFFRACTION100
4.3404-5.46720.15731510.12972698X-RAY DIFFRACTION95
5.4672-47.4540.1931540.18532961X-RAY DIFFRACTION98
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)
10.04340.01160.00340.0205-0.04230.04770.02890.12030.1987-0.2357-0.1275-0.37590.18860.34240.00010.58520.0510.08180.33350.02340.3765125.90722.6362-8.1191
20.8076-0.2791-0.26810.2881-0.12170.25550.07580.05580.3075-0.31630.10350.12010.2764-0.14360.14810.5475-0.0984-0.10170.32760.07180.2932107.992218.2584-5.5702
30.12010.06610.14990.10880.15440.3236-0.14360.0883-0.0051-0.35770.57380.35640.431-0.29880.2237-0.3385-0.7374-0.74810.3286-0.09010.36994.553918.1451.6877
40.125-0.0760.00090.03550.00270.1850.12640.07650.0616-0.21010.16220.28240.0807-0.52170.18490.3645-0.082-0.19090.52080.22070.520997.774433.6339-3.6537
50.878-0.3291-0.03990.5211-0.55770.83880.0038-0.17820.0143-0.18040.12960.06510.3713-0.19610.06830.3549-0.0921-0.09930.22430.02210.2522111.257220.37453.4087
60.1314-0.21680.16410.1328-0.16310.13740.0421-0.0218-0.0737-0.12480.0035-0.10170.1513-0.018900.34380.0204-0.02770.33070.04180.414127.956612.97612.5177
70.07070.0159-0.02920.0325-0.01440.02630.40910.3974-0.397-0.3775-0.30040.67710.2196-0.1591-0.0020.55530.1175-0.18360.4826-0.12020.4462107.380547.1301-30.0057
80.40870.26360.21690.37040.18090.30130.38280.68650.0478-0.2422-0.4399-0.60340.14860.46020.1580.25190.15090.33920.79060.33930.3892134.695955.7447-28.7339
90.1905-0.1206-0.06040.1150.00420.08280.29730.3386-0.099-0.2516-0.2985-0.17530.1820.42940.07020.48870.24440.16580.57450.02180.3852136.797538.9114-27.4432
100.6359-0.31440.30210.5434-0.06910.11040.16880.1860.062-0.1138-0.315-0.04910.04270.1773-0.00140.26780.06020.04810.33780.04010.2502122.972753.9721-21.0606
110.3474-0.30160.34460.5013-0.36280.2270.12030.15190.0807-0.1981-0.18170.13020.05760.1214-0.00410.28850.05750.0090.3224-0.01830.2522118.300753.2521-19.9604
120.0921-0.0747-0.04340.0825-0.02830.05070.0524-0.0558-0.05840.1555-0.01170.20440.0339-0.2673-00.30590.04120.00760.358-0.00290.5224100.333159.5956-14.2908
130.0040.00220.0030.00270.0030.0016-0.04770.01270.058-0.0433-0.02250.0089-0.02320.0299-00.6314-0.0788-0.01140.6410.04590.5269107.201110.98388.3312
140.00210.0002-0.00160.01220.0030.0011-0.0428-0.0230.0318-0.014-0.0427-0.01370.03290.03190.00010.63280.00850.03820.879-0.19021.215126.141862.6828-18.6713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 291 )
6X-RAY DIFFRACTION6chain 'A' and (resid 292 through 354 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 252 )
11X-RAY DIFFRACTION11chain 'B' and (resid 253 through 317 )
12X-RAY DIFFRACTION12chain 'B' and (resid 318 through 355 )
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 29 )
14X-RAY DIFFRACTION14chain 'D' and (resid 24 through 28 )

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