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- PDB-2ot7: Crystal structure of JMJD2A complexed with histone H3 peptide mon... -

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Basic information

Entry
Database: PDB / ID: 2ot7
TitleCrystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9
Components
  • JmjC domain-containing histone demethylation protein 3A
  • histone 3 K9 monomethyl
KeywordsOXIDOREDUCTASE / Fe / double-stranded beta helix / demethylase / oxygenase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine36 demethylase / histone H3-tri/dimethyl-lysine-36 demethylase activity / histone demethylation / histone H3-K36 demethylation / histone H3-methyl-lysine-36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3-tri/dimethyl-lysine-9 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / Chromatin modifying enzymes ...[histone H3]-trimethyl-L-lysine36 demethylase / histone H3-tri/dimethyl-lysine-36 demethylase activity / histone demethylation / histone H3-K36 demethylation / histone H3-methyl-lysine-36 demethylase activity / cardiac muscle hypertrophy in response to stress / histone H3-tri/dimethyl-lysine-9 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / negative regulation of histone H3-K9 trimethylation / Chromatin modifying enzymes / regulation of gene expression, epigenetic / histone H3-K9 demethylation / histone H3-methyl-lysine-9 demethylase activity / negative regulation of astrocyte differentiation / pericentric heterochromatin / Interleukin-7 signaling / telomere organization / histone demethylase activity / RNA Polymerase I Promoter Opening / DNA replication-dependent chromatin assembly / Assembly of the ORC complex at the origin of replication / DNA methylation / negative regulation of cell death / SIRT1 negatively regulates rRNA expression / negative regulation of autophagy / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / chromatin organization => GO:0006325 / HCMV Late Events / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / methylated histone binding / nuclear chromosome / positive regulation of neuron differentiation / NoRC negatively regulates rRNA expression / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / response to nutrient levels / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RMTs methylate histone arginines / HDMs demethylate histones / nucleosome assembly / Meiotic recombination / Pre-NOTCH Transcription and Translation / PKMTs methylate histone lysines / HCMV Early Events / fibrillar center / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromatin remodeling / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of gene expression / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / membrane / nucleoplasm / nucleus / cytosol
Similarity search - Function
Jumonji domain-containing protein 2A Tudor domain / Lysine-specific demethylase 4, Tudor domain / Tudor domain / Tudor domain / Small domain found in the jumonji family of transcription factors / jmjN domain / JmjN domain profile. / JmjN domain / Extended PHD (ePHD) domain profile. / Extended PHD (ePHD) domain ...Jumonji domain-containing protein 2A Tudor domain / Lysine-specific demethylase 4, Tudor domain / Tudor domain / Tudor domain / Small domain found in the jumonji family of transcription factors / jmjN domain / JmjN domain profile. / JmjN domain / Extended PHD (ePHD) domain profile. / Extended PHD (ePHD) domain / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / PHD zinc finger / Zinc finger, PHD-type / Histone-fold / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lysine-specific demethylase 4A / NICKEL (II) ION / N-OXALYLGLYCINE / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.135 Å
AuthorsKavanagh, K.L. / Ng, S.S. / Pilka, E. / McDonough, M.A. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. ...Kavanagh, K.L. / Ng, S.S. / Pilka, E. / McDonough, M.A. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Schofield, C.J. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: 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
DepositionFeb 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jun 29, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / diffrn_source / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _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_ref_seq_dif.details / _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: JmjC domain-containing histone demethylation protein 3A
B: JmjC domain-containing histone demethylation protein 3A
C: histone 3 K9 monomethyl
D: histone 3 K9 monomethyl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,91710
Polymers90,3754
Non-polymers5426
Water4,738263
1
A: JmjC domain-containing histone demethylation protein 3A
C: histone 3 K9 monomethyl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers45,1872
Non-polymers2713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JmjC domain-containing histone demethylation protein 3A
D: histone 3 K9 monomethyl
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4585
Polymers45,1872
Non-polymers2713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.209, 149.842, 57.470
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 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: JMJD2A, JHDM3A, JMJD2, KIAA0677 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
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 3 K9 monomethyl


Mass: 860.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic H3 peptide monomethylated at K9. Its sequence is based on human histone H3 fragment (residues 7-14), gene HIST1H3A
References: UniProt: P68431*PLUS

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Non-polymers , 4 types, 269 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-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3350, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.135→83.92 Å / Num. all: 48784 / Num. obs: 48784 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.9
Reflection shellResolution: 2.135→2.25 Å / Redundancy: 3 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2 / Num. unique all: 7095 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OQ7
Resolution: 2.135→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.989 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24072 2031 4.2 %RANDOM
Rwork0.18676 ---
all0.18909 45914 --
obs0.18909 45914 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.416 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.135→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 24 263 6017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225929
X-RAY DIFFRACTIONr_bond_other_d0.0010.024080
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9468036
X-RAY DIFFRACTIONr_angle_other_deg0.8973.0019871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97123.309272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42215959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.221532
X-RAY DIFFRACTIONr_chiral_restr0.0770.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021296
X-RAY DIFFRACTIONr_nbd_refined0.1960.21117
X-RAY DIFFRACTIONr_nbd_other0.1830.24003
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22838
X-RAY DIFFRACTIONr_nbtor_other0.0850.22901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.38433719
X-RAY DIFFRACTIONr_mcbond_other0.63231427
X-RAY DIFFRACTIONr_mcangle_it3.33155740
X-RAY DIFFRACTIONr_scbond_it5.16572667
X-RAY DIFFRACTIONr_scangle_it6.362112295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.135→2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 166 -
Rwork0.295 3383 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.4716-0.79080.48831.9986-0.38450.93430.13410.2923-0.0292-0.2758-0.1770.15190.03590.10940.0428-0.12630.02250.0106-0.0863-0.0124-0.1478-30.3943-22.1087-22.9005
22.1617-0.4169-0.07512.1003-0.37581.7530.08780.01760.0506-0.29710.0223-0.20670.2343-0.12-0.1101-0.0888-0.0379-0.0379-0.18530.0146-0.1148-37.9127-54.81152.3462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 355
2X-RAY DIFFRACTION2B7 - 354

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