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- PDB-5fxw: Crystal structure of JmjC domain of human histone demethylase UTY... -

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Basic information

Entry
Database: PDB / ID: 5fxw
TitleCrystal structure of JmjC domain of human histone demethylase UTY in complex with fumarate
ComponentsHISTONE DEMETHYLASE UTY
KeywordsTRANSFERASE / TCA INTERMEDIATE
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
FUMARIC ACID / : / Histone demethylase UTY
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsNowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with Fumarate
Authors: Nowak, R. / Krojer, T. / Johansson, C. / Gileadi, C. / Kupinska, K. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U.
History
DepositionMar 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 2.0Jun 14, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _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_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.pdbx_dist_value / _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
Revision 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)111,41723
Polymers110,0132
Non-polymers1,40421
Water10,575587
1
A: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,67711
Polymers55,0061
Non-polymers67110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEMETHYLASE UTY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,73912
Polymers55,0061
Non-polymers73311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.630, 109.440, 118.210
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) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14607

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Non-polymers , 5 types, 608 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.89 Å3/Da / Density % sol: 57.49 % / Description: NONE
Crystal growpH: 7.8
Details: 0.1M HEPES PH 7.8 -- 0.25M TRIMETHYLAMINE N-OXIDE -- 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.09→54.72 Å / Num. obs: 69482 / % possible obs: 98.9 % / Observed criterion σ(I): 1.2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZLI

3zli


Resolution: 2.09→54.72 Å / σ(F): 1.34 / Stereochemistry target values: ML / Details: DISORDERED SIDE CHAINS WERE REMOVED
RfactorNum. reflection% reflection
Rfree0.2455 3412 4.9 %
Rwork0.1921 --
obs0.1947 69283 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→54.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7017 0 80 587 7684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.11990.3491400.33292741X-RAY DIFFRACTION100
2.1199-2.15150.39081530.30282749X-RAY DIFFRACTION100
2.1515-2.18510.35761290.30452742X-RAY DIFFRACTION100
2.1851-2.2210.3331710.29272712X-RAY DIFFRACTION100
2.221-2.25930.6061160.43652199X-RAY DIFFRACTION80
2.2593-2.30040.31051430.28662572X-RAY DIFFRACTION94
2.3004-2.34460.31131460.2542710X-RAY DIFFRACTION100
2.3446-2.39250.31051660.23982750X-RAY DIFFRACTION100
2.3925-2.44450.30471460.22242760X-RAY DIFFRACTION100
2.4445-2.50130.28631210.21112761X-RAY DIFFRACTION100
2.5013-2.56390.26471190.20532772X-RAY DIFFRACTION100
2.5639-2.63320.27511520.20592774X-RAY DIFFRACTION100
2.6332-2.71070.26661320.22682754X-RAY DIFFRACTION100
2.7107-2.79820.26621370.19512763X-RAY DIFFRACTION100
2.7982-2.89820.26971480.1872779X-RAY DIFFRACTION100
2.8982-3.01420.25851560.19862767X-RAY DIFFRACTION100
3.0142-3.15140.26421390.18982787X-RAY DIFFRACTION100
3.1514-3.31750.22021340.18372791X-RAY DIFFRACTION100
3.3175-3.52530.25441250.18912798X-RAY DIFFRACTION99
3.5253-3.79750.22821460.1812751X-RAY DIFFRACTION99
3.7975-4.17950.20611290.15752788X-RAY DIFFRACTION98
4.1795-4.7840.19911650.13082812X-RAY DIFFRACTION100
4.784-6.02610.1641490.1442857X-RAY DIFFRACTION100
6.0261-54.73870.16141500.14212982X-RAY DIFFRACTION100

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