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- PDB-5fwe: JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5fwe
TitleJMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE
Components
  • LYSINE-SPECIFIC DEMETHYLASE 4A
  • SYNTHETIC PEPTIDEPeptide synthesis
KeywordsOXIDOREDUCTASE / JMJD2A / 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 / 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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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 / telomere organization / positive regulation of neuron differentiation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / response to nutrient levels / negative regulation of autophagy / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / Amyloid fiber formation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / protein-containing complex / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4A / Histone H4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChowdhury, R. / Walport, L.J. / Schofield, C.J.
CitationJournal: Nat.Commun. / Year: 2016
Title: Arginine Demethylation is Catalysed by a Subset of Jmjc Histone Lysine Demethylases.
Authors: Walport, L.J. / Hopkinson, R.J. / Chowdhury, R. / Schiller, R. / Ge, W. / Kawamura, A. / Schofield, C.J.
History
DepositionFeb 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Jan 10, 2024Group: 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: SYNTHETIC PEPTIDE
D: SYNTHETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,99313
Polymers91,2884
Non-polymers7059
Water7,044391
1
B: LYSINE-SPECIFIC DEMETHYLASE 4A
D: SYNTHETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0437
Polymers45,6442
Non-polymers3995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-22.2 kcal/mol
Surface area15350 Å2
MethodPISA
2
A: LYSINE-SPECIFIC DEMETHYLASE 4A
C: SYNTHETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9506
Polymers45,6442
Non-polymers3074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-22.7 kcal/mol
Surface area15340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.739, 149.400, 57.372
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 / ...JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A / JUMONJI DOMAIN-CONTAINING PROTEIN 2A / JUMONJI DOMAIN CONTAINING PROTEIN 2A


Mass: 44326.273 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
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 SYNTHETIC PEPTIDE / Peptide synthesis


Mass: 1317.521 Da / Num. of mol.: 2 / Fragment: HISTONE H4(1-15)R3ME2S PEPTIDE, UNP RESIDUES 2-16 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P62805

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Non-polymers , 6 types, 400 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-OGA / N-OXALYLGLYCINE / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.64 Å3/Da / Density % sol: 53.44 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 2.05→49.85 Å / Num. obs: 54997 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 33.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OX0

2ox0


Resolution: 2.05→49.854 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 2709 4.9 %
Rwork0.2342 --
obs0.2357 54928 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---1.51 Å20 Å2
3---2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 32 391 6063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065988
X-RAY DIFFRACTIONf_angle_d0.7798132
X-RAY DIFFRACTIONf_dihedral_angle_d14.1213542
X-RAY DIFFRACTIONf_chiral_restr0.044843
X-RAY DIFFRACTIONf_plane_restr0.0041059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0496-2.08690.29281200.29242598X-RAY DIFFRACTION96
2.0869-2.1270.3451490.28142736X-RAY DIFFRACTION100
2.127-2.17040.33591540.27342687X-RAY DIFFRACTION100
2.1704-2.21760.28691600.26722712X-RAY DIFFRACTION100
2.2176-2.26920.27291240.2482746X-RAY DIFFRACTION100
2.2692-2.3260.30941500.24242716X-RAY DIFFRACTION100
2.326-2.38890.3081470.24182735X-RAY DIFFRACTION100
2.3889-2.45910.27331330.23062733X-RAY DIFFRACTION100
2.4591-2.53850.28081560.22352709X-RAY DIFFRACTION100
2.5385-2.62920.27211570.2312739X-RAY DIFFRACTION100
2.6292-2.73450.2511420.21732699X-RAY DIFFRACTION98
2.7345-2.85890.26171320.21532747X-RAY DIFFRACTION100
2.8589-3.00970.25611380.212753X-RAY DIFFRACTION100
3.0097-3.19820.19421340.1942788X-RAY DIFFRACTION100
3.1982-3.44510.22661370.18832758X-RAY DIFFRACTION100
3.4451-3.79160.21771360.18062802X-RAY DIFFRACTION100
3.7916-4.340.17551470.15872805X-RAY DIFFRACTION100
4.34-5.46690.14641380.14492778X-RAY DIFFRACTION98
5.4669-49.86870.20191550.1872978X-RAY DIFFRACTION100

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