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- PDB-4uf0: Crystal structure of JmjC domain of human histone demethylase UTY... -

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Basic information

Entry
Database: PDB / ID: 4uf0
TitleCrystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.
Components(HISTONE DEMETHYLASE ...) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone demethylase activity / HDMs demethylate histones / chromatin DNA binding / regulation of gene expression / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Tetratricopeptide repeat / Tetratricopeptide repeat ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1370 / Cysteine Rich Protein - #20 / : / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cysteine Rich Protein / Tetratricopeptide repeat / Tetratricopeptide repeat / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Chem-MMK / Histone demethylase UTY
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSrikannathasan, V. / Johansson, C. / Gileadi, C. / Tobias, K. / Kopec, J. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, ...Authors: Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U.
History
DepositionDec 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Jun 1, 2016Group: Database references
Revision 1.4Jun 29, 2016Group: Database references
Revision 1.5Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.6Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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.pdbx_dist_value / _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_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_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: HISTONE DEMETHYLASE UTY
B: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,12428
Polymers110,0282
Non-polymers2,09726
Water8,791488
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A: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,94512
Polymers55,0201
Non-polymers92411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,18016
Polymers55,0071
Non-polymers1,17215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.494, 110.458, 119.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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HISTONE DEMETHYLASE ... , 2 types, 2 molecules AB

#1: Protein HISTONE DEMETHYLASE UTY / UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME / UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME ...UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME / UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN


Mass: 55020.430 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 878-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-CT10HF-LIC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O14607, 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 HISTONE DEMETHYLASE UTY / UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME / UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME ...UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN ON THE Y CHROMOSOME / UBIQUITOUSLY-TRANSCRIBED Y CHROMOSOME TETRATRICOPEPTIDE REPEAT PROTEIN


Mass: 55007.387 Da / Num. of mol.: 1 / Fragment: JMJC DOMAIN, RESIDUES 878-1347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-CT10HF-LIC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O14607, 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

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Non-polymers , 5 types, 514 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-MMK / 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid


Mass: 306.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N4O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE (MMK): DIMETHYLAMINE GROUP DID NOT SHOW ANY DENSITY SO ...5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE (MMK): DIMETHYLAMINE GROUP DID NOT SHOW ANY DENSITY SO REFINED WITH ZERO OCCUPANCY

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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: 2.83 Å3/Da / Density % sol: 56.56 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% PEG3350, 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2014 / Details: ADSC QUANTUM 315
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.78→81.03 Å / Num. obs: 114771 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.51
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.86 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZLI

3zli


Resolution: 1.78→81.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.892 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES REFINED INDIVIDUALLY DIMETHYLAMINE GROUP OF THE DRG LIGAND OCCUPANCY WAS SET UP TO ZERO AS WE DO NOT SEE ANY DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.21517 5650 4.9 %RANDOM
Rwork0.14857 ---
obs0.15184 109117 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2--0.49 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.78→81.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7058 0 128 488 7674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197368
X-RAY DIFFRACTIONr_bond_other_d0.0030.026969
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9429993
X-RAY DIFFRACTIONr_angle_other_deg0.9093.00115996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48924.645338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89151217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5611531
X-RAY DIFFRACTIONr_chiral_restr0.1010.21095
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021742
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3593.343532
X-RAY DIFFRACTIONr_mcbond_other5.3583.3413530
X-RAY DIFFRACTIONr_mcangle_it6.025.0164408
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0723.8213836
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.47814337
X-RAY DIFFRACTIONr_sphericity_free28.3135190
X-RAY DIFFRACTIONr_sphericity_bonded18.00814467
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 377 -
Rwork0.214 8019 -
obs--99.99 %

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