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- PDB-3zli: Crystal structure of JmjC domain of human histone demethylase UTY -

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Basic information

Entry
Database: PDB / ID: 3zli
TitleCrystal structure of JmjC domain of human histone demethylase UTY
ComponentsHISTONE DEMETHYLASE UTY
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 / heart development / 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 / Cupin ...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 / Cupin / Tetratricopeptide repeat / 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
2-OXOGLUTARIC ACID / : / Histone demethylase UTY
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVollmar, M. / Gileadi, C. / Shrestha, L. / Goubin, S. / Johansson, C. / Krojer, T. / Raynor, J.W. / Bradley, A. / von Delft, F. / Arrowsmith, C.H. ...Vollmar, M. / Gileadi, C. / Shrestha, L. / Goubin, S. / Johansson, C. / Krojer, T. / Raynor, J.W. / Bradley, A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Human Uty(Kdm6C) is a Male-Specific Nepsilon-Methyl Lysyl Demethylase.
Authors: Walport, L.J. / Hopkinson, R.J. / Vollmar, M. / Madden, S.K. / Gileadi, C. / Oppermann, U. / Schofield, C.J. / Johansson, C.
History
DepositionJan 31, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.2May 20, 2015Group: Database references / Other
Revision 1.3Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)111,41622
Polymers110,0132
Non-polymers1,40420
Water9,890549
1
A: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,77012
Polymers55,0061
Non-polymers76411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,64610
Polymers55,0061
Non-polymers6409
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.585, 110.249, 118.242
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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Protein , 1 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: 55006.402 Da / Num. of mol.: 2 / 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, 569 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.69 Å3/Da / Density % sol: 54.31 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M TRIMETHYLAMINE N-OXIDE; 0.1M HEPES PH 7.5; 10%(W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→49.96 Å / Num. obs: 110147 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AVS

3avs


Resolution: 1.8→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.5 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20435 5494 5 %RANDOM
Rwork0.17599 ---
obs0.17741 104567 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: 32.803 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å20 Å2
2---0.05 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 80 549 7656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197387
X-RAY DIFFRACTIONr_bond_other_d0.0050.026905
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9410076
X-RAY DIFFRACTIONr_angle_other_deg1.081315861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31824.74346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8211531
X-RAY DIFFRACTIONr_chiral_restr0.0970.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218432
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021767
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_it1.8452.2463556
X-RAY DIFFRACTIONr_mcbond_other1.8432.2463555
X-RAY DIFFRACTIONr_mcangle_it2.6323.3554448
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5592.5453831
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 391 -
Rwork0.26 7693 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8897-0.06620.02240.89840.36570.73850.0509-0.05440.0844-0.0581-0.0812-0.0144-0.015-0.07610.03030.0166-0.01090.00330.0376-0.0210.0471-17.6981-4.120424.5041
21.98520.18610.45430.5820.14150.23970.1653-0.113-0.12530.0697-0.1008-0.04370.0445-0.0103-0.06450.0353-0.0267-0.01590.0393-0.00020.06468.756-22.155619.1423
30.8201-0.0311-0.24370.9508-0.37790.92480.0873-0.0193-0.1148-0.04370.04070.2283-0.0350.0218-0.1280.0236-0.0102-0.03780.04380.00240.1116-38.7019-48.655522.6361
43.3997-1.25651.56051.0568-0.97370.98230.15070.3718-0.0216-0.1043-0.1869-0.06030.10090.20130.03620.0630.0616-0.03710.1617-0.03820.0422-11.7811-47.62833.5356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A882 - 1190
2X-RAY DIFFRACTION2A1191 - 1344
3X-RAY DIFFRACTION3B881 - 1217
4X-RAY DIFFRACTION4B1218 - 1344

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