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Basic information

Entry
Database: PDB / ID: 2xue
TitleCRYSTAL STRUCTURE OF JMJD3
ComponentsLYSINE-SPECIFIC DEMETHYLASE 6B
KeywordsOXIDOREDUCTASE / HISTONE METHYLASE
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / response to fungicide ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / histone demethylase activity / cell fate commitment / response to fungicide / Chromatin modifications during the maternal to zygotic transition (MZT) / response to activity / hippocampus development / HDMs demethylate histones / chromatin DNA binding / beta-catenin binding / cellular response to hydrogen peroxide / positive regulation of cold-induced thermogenesis / regulation of gene expression / Oxidative Stress Induced Senescence / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / 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 / JmjC domain, hydroxylase ...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 / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribbon / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Lysine-specific demethylase 6B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsChung, C. / Rowland, P. / Mosley, J. / Thomas, P.J.
CitationJournal: Nature / Year: 2012
Title: A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response
Authors: Kruidenier, L. / Chung, C. / Cheng, Z. / Liddle, J. / Che, K. / Joberty, G. / Bantscheff, M. / Bountra, C. / Bridges, A. / Diallo, H. / Eberhard, D. / Hutchinson, S. / Jones, E. / Katso, R. ...Authors: Kruidenier, L. / Chung, C. / Cheng, Z. / Liddle, J. / Che, K. / Joberty, G. / Bantscheff, M. / Bountra, C. / Bridges, A. / Diallo, H. / Eberhard, D. / Hutchinson, S. / Jones, E. / Katso, R. / Leveridge, M. / Mander, P.K. / Mosley, J. / Ramirez-Molina, C. / Rowland, P. / Schofield, C.J. / Sheppard, R.J. / Smith, J.E. / Swales, C. / Tanner, R. / Thomas, P. / Tumber, A. / Drewes, G. / Oppermann, U. / Patel, D.J. / Lee, K. / Wilson, D.M.
History
DepositionOct 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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.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 / _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: LYSINE-SPECIFIC DEMETHYLASE 6B
B: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,56510
Polymers115,8382
Non-polymers7278
Water10,088560
1
A: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2835
Polymers57,9191
Non-polymers3634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2835
Polymers57,9191
Non-polymers3634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.215, 65.154, 77.462
Angle α, β, γ (deg.)86.09, 67.19, 68.26
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LYSINE-SPECIFIC DEMETHYLASE 6B / JMJD3 / JMJC DOMAIN-CONTAINING PROTEIN 3 / JUMONJI DOMAIN-CONTAINING PROTEIN 3 / LYSINE DEMETHYLASE 6B


Mass: 57919.098 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 1138-1640
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: O15054, 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, 568 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.53 Å3/Da / Density % sol: 51.04 % / Description: NONE
Crystal growpH: 8.5
Details: MORPHEUS SCREEN (MOLECULAR DIMENSIONS) CONDITION A12 (0.03M MGCL2, 0.03M CACL2, 0.1M TRIS HCL/BICINE PH 8.5, 12.5%V/V MPD, 12.5%W/V PEG1000, 12.5%W/V PEG3350)

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID14-410.981
SYNCHROTRONESRF ID14-420.9795
Detector
TypeIDDetectorDate
ADSC CCD1CCDApr 28, 2010
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9811
20.97951
ReflectionResolution: 2→40 Å / Num. obs: 61840 / % possible obs: 89.9 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.5 / % possible all: 56.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RESOLVEphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→71.13 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.488 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21574 2450 4 %RANDOM
Rwork0.17932 ---
obs0.18081 59387 89.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-2.46 Å2-1.11 Å2
2--1.4 Å21.85 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→71.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6805 0 34 560 7399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227068
X-RAY DIFFRACTIONr_bond_other_d0.0010.024722
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9359612
X-RAY DIFFRACTIONr_angle_other_deg0.8063.00111455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4855852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90123.761335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.713151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0191546
X-RAY DIFFRACTIONr_chiral_restr0.0630.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217852
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021468
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_it0.87624262
X-RAY DIFFRACTIONr_mcbond_other0.09821712
X-RAY DIFFRACTIONr_mcangle_it1.72246917
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02542806
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.07262695
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: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 103 -
Rwork0.29 2822 -
obs--57.31 %
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)
10.6615-0.33220.42440.3081-0.32040.6222-0.0007-0.018-0.0178-0.00380.01150.0061-0.0018-0.0344-0.01070.0336-0.01470.00090.0185-0.01510.024957.160117.094-13.7037
20.594-0.24170.22470.4552-0.27520.5281-0.01080.0028-0.0064-0.03680.0224-0.03260.0502-0.0428-0.01160.0355-0.01030.01160.0116-0.01110.023574.702745.692319.3965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1178 - 4000
2X-RAY DIFFRACTION2B1181 - 4000

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