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- PDB-2ybs: JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 P... -

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Basic information

Entry
Database: PDB / ID: 2ybs
TitleJMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41)
Components
  • HISTONE H3.1T
  • LYSINE-SPECIFIC DEMETHYLASE 4A
KeywordsOXIDOREDUCTASE/PEPTIDE / OXIDOREDUCTASE-PEPTIDE COMPLEX / NON-HEME IRON / DIOXYGENASE / DOUBLE-STRANDED BETA HELIX / DSBH / FACIAL TRIAD / METAL BINDING PROTEIN / EPIGENETIC AND TRANSCRIPTION REGULATION / CHROMATIN REGULATOR / HYDROXYLATION
Function / homology
Function and homology information


spermatogonial cell division / [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / DNA replication-dependent chromatin assembly / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity ...spermatogonial cell division / [histone H3]-trimethyl-L-lysine36 demethylase / histone H3K36me2/H3K36me3 demethylase activity / histone H4K20me2 reader activity / histone H3K36 demethylase activity / DNA replication-dependent chromatin assembly / cardiac muscle hypertrophy in response to stress / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / histone H3K9 demethylase activity / regulation of cell differentiation / histone demethylase activity / pericentric heterochromatin / heterochromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / negative regulation of autophagy / Meiotic synapsis / Condensation of Prophase Chromosomes / condensed nuclear chromosome / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / HDMs demethylate histones / G2/M DNA damage checkpoint / 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 / 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 / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / (2S)-2-HYDROXYPENTANEDIOIC ACID / Lysine-specific demethylase 4A / Histone H3.1t
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsChowdhury, R. / Schofield, C.J.
CitationJournal: EMBO Rep. / Year: 2011
Title: The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.
Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, ...Authors: Chowdhury, R. / Yeoh, K.K. / Tian, Y.M. / Hillringhaus, L. / Bagg, E.A. / Rose, N.R. / Leung, I.K. / Li, X.S. / Woon, E.C. / Yang, M. / McDonough, M.A. / King, O.N. / Clifton, I.J. / Klose, R.J. / Claridge, T.D. / Ratcliffe, P.J. / Schofield, C.J. / Kawamura, A.
History
DepositionMar 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 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_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
D: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,00211
Polymers91,3664
Non-polymers6377
Water8,557475
1
A: LYSINE-SPECIFIC DEMETHYLASE 4A
C: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0476
Polymers45,6832
Non-polymers3644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-7.6 kcal/mol
Surface area15990 Å2
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 4A
D: HISTONE H3.1T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9555
Polymers45,6832
Non-polymers2723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-7.5 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.924, 149.354, 57.271
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 / 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: 1356.615 Da / Num. of mol.: 2 / Fragment: HISTONE H3K36ME3 PEPTIDE, RESIDUES 31-42 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16695

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Non-polymers , 5 types, 482 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-S2G / (2S)-2-HYDROXYPENTANEDIOIC ACID


Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 1 IN UNP Q16695 IS AN INITIATOR METHIONINE AND IS REMOVED.

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M CITRATE PH 5.5, 4 MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 26, 2010 / Details: VARIMAX HF
RadiationMonochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→30.14 Å / Num. obs: 36569 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.69
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.26 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OX0

2ox0


Resolution: 2.32→30.14 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 610327.83 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ALTHOUGH THE LIGAND, S2G WAS MODELLED WITH FULL OCCUPANCY, ADDITIONAL POSITIVE DIFFERENCE DENSITY NEAR THE LIGAND BINDING SITE WAS SUGGESTIVE OF A POSSIBLE LOW OCCUPANCY ALTERNATE ...Details: ALTHOUGH THE LIGAND, S2G WAS MODELLED WITH FULL OCCUPANCY, ADDITIONAL POSITIVE DIFFERENCE DENSITY NEAR THE LIGAND BINDING SITE WAS SUGGESTIVE OF A POSSIBLE LOW OCCUPANCY ALTERNATE CONFORMATION OR A BUFFER MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3343 9.1 %RANDOM
Rwork0.214 ---
obs0.214 36569 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9247 Å2 / ksol: 0.308558 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.52 Å20 Å20 Å2
2--3.9 Å20 Å2
3---0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.32→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 30 475 6395
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.32→2.4 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.315 274 10.2 %
Rwork0.259 2407 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4S2G.PARS2G.TOP
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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