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- PDB-2ybp: JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 P... -

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Basic information

Entry
Database: PDB / ID: 2ybp
TitleJMJD2A COMPLEXED WITH R-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


[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 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / methylated histone binding / Inhibition of DNA recombination at telomere / 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 / nucleosome assembly / structural constituent of chromatin / nucleosome / 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 / positive regulation of gene expression / 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. / 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
(2R)-2-hydroxypentanedioic acid / NICKEL (II) ION / Lysine-specific demethylase 4A / Histone H3.1t
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsChowdhury, R. / McDonough, M.A. / 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 9, 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 / Structure summary / Category: audit_author / citation / citation_author
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
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
Water10,989610
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 area2180 Å2
ΔGint-20.4 kcal/mol
Surface area15710 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 area2030 Å2
ΔGint-20.7 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.291, 149.668, 57.319
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, 617 molecules

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


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2HG / (2R)-2-hydroxypentanedioic acid


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


Mass: 18.015 Da / Num. of mol.: 610 / 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: 0.1M 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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.02→45.51 Å / Num. obs: 63521 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.4
Reflection shellResolution: 2.02→2.06 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % 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: 2.02→45.51 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 92231.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ALTHOUGH THE LIGAND, 2HG 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, 2HG 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
Rfree0.225 5515 8.7 %RANDOM
Rwork0.201 ---
obs0.201 63521 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4798 Å2 / ksol: 0.334292 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2--3.76 Å20 Å2
3----1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.02→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 0 30 610 6511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
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
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.02→2.06 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.294 278 10.1 %
Rwork0.283 2410 -
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 DIFFRACTION4R2G.PARR2G.TOP
X-RAY DIFFRACTION5GOL.PARGOL.TOP

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