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- PDB-2xxz: Crystal structure of the human JMJD3 jumonji domain -

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Basic information

Entry
Database: PDB / ID: 2xxz
TitleCrystal structure of the human JMJD3 jumonji domain
ComponentsLYSINE-SPECIFIC DEMETHYLASE 6B
KeywordsOXIDOREDUCTASE / HISTONE DEMETHYLATION / OXYGENASE / CHROMATIN MODIFICATION
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
: / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. ...: / : / : / Lysine-specific demethylase 6/UTY, C-terminal helical domain / KDM6, GATA-like / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
8-hydroxyquinoline-5-carboxylic acid / NICKEL (II) ION / Lysine-specific demethylase 6B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChe, K.H. / Yue, W.W. / Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Tumber, A. / Daniel, M. / Burgess-Brown, N. / Savitsky, P. / Ugochukwu, E. ...Che, K.H. / Yue, W.W. / Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Tumber, A. / Daniel, M. / Burgess-Brown, N. / Savitsky, P. / Ugochukwu, E. / Filippakopoulos, P. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Human Jmjd3 Jumonji Domain
Authors: Che, K.H. / Yue, W.W. / Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Tumber, A. / Daniel, M. / Burgess-Brown, N. / Savitsky, P. / von Delft, F. / Ugochukwu, E. / Filippakopoulos, P. / Arrowsmith, ...Authors: Che, K.H. / Yue, W.W. / Krojer, T. / Muniz, J.R.C. / Ng, S.S. / Tumber, A. / Daniel, M. / Burgess-Brown, N. / Savitsky, P. / von Delft, F. / Ugochukwu, E. / Filippakopoulos, P. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionNov 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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_asym_id / _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.ptnr1_symmetry / _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_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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)76,26213
Polymers75,3742
Non-polymers88811
Water5,747319
1
A: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2659
Polymers37,6871
Non-polymers5788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSINE-SPECIFIC DEMETHYLASE 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9974
Polymers37,6871
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.757, 71.431, 159.698
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 LYSINE-SPECIFIC DEMETHYLASE 6B / JMJD3 / JMJC DOMAIN-CONTAINING PROTEIN 3 / JUMONJI DOMAIN-CONTAINING PROTEIN 3 / LYSINE DEMETHYLASE 6B


Mass: 37686.949 Da / Num. of mol.: 2 / Fragment: JUMONJI DOMAIN, RESIDUES 1173-1502
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)-R3-PRARE2
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, 330 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-8XQ / 8-hydroxyquinoline-5-carboxylic acid


Mass: 189.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.17 Å3/Da / Density % sol: 43.3 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→29.16 Å / Num. obs: 61104 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→29.16 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.236 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21578 3016 5 %RANDOM
Rwork0.18324 ---
obs0.18486 61100 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.882 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--1.26 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 52 319 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214906
X-RAY DIFFRACTIONr_bond_other_d0.0010.023250
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9316714
X-RAY DIFFRACTIONr_angle_other_deg1.05337900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91324.095232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37415761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6311527
X-RAY DIFFRACTIONr_chiral_restr0.0870.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021006
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_it1.68832949
X-RAY DIFFRACTIONr_mcbond_other0.40431178
X-RAY DIFFRACTIONr_mcangle_it2.87154804
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.10571957
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.069111902
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→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 265 -
Rwork0.333 4968 -
obs--99.6 %
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)
10.94210.4975-0.01450.9109-0.53951.5247-0.00880.0763-0.0191-0.0143-0.0187-0.02210.12250.07940.02750.12210.00210.00540.1863-0.0150.153349.900748.2989-13.8463
20.92880.21860.0690.632-0.40782.1837-0.0125-0.05640.05420.07830.00890.0193-0.1193-0.04520.00370.08210.0026-0.00060.22050.00650.176151.991754.465510.4149
36.2658-0.63551.10183.2935-2.79493.9547-0.2004-0.5539-0.59010.11860.1108-0.06870.91930.28530.08950.65950.1830.03680.21470.06340.169250.358826.00879.8115
42.84040.78020.2241.6504-0.20820.8267-0.0158-0.1324-0.17120.1060.0501-0.07920.15850.0094-0.03430.1433-0.00050.00150.22510.0230.162157.111243.747518.2481
50.4915-0.23750.26760.4974-0.03371.3970.0089-0.0481-0.03370.03880.00020.05710.1048-0.1377-0.00910.0967-0.01960.00580.1790.00670.173743.932246.47340.7549
60.7773-0.3633-0.00481.54650.43812.03690.024-0.02740.03440.0251-0.05740.07680.1793-0.14240.03340.1437-0.0160.01440.207-0.0120.144145.140548.7691-24.771
71.59211.71650.83512.16190.45081.9935-0.31250.23020.1558-0.54740.26170.2052-0.0721-0.06320.05070.2845-0.0666-0.06990.22450.02850.14442.598354.9251-48.0549
81.56281.36230.63052.43980.76721.5072-0.28740.27740.0317-0.60070.2210.0365-0.1097-0.01940.06640.2733-0.0602-0.00740.2152-0.01230.085842.372948.8428-49.7312
90.44530.09740.48311.38470.10021.9709-0.01940.0481-0.0411-0.17350.03020.00140.19620.0161-0.01080.2052-0.00510.00020.1149-0.01420.134944.982140.814-38.8798
102.07760.4432.14063.71150.4135.5379-0.03690.2432-0.0511-0.056-0.1332-0.2793-0.37450.51310.17010.1075-0.0099-0.02020.26490.0250.216363.567158.4688-24.1731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1175 - 1212
2X-RAY DIFFRACTION2A1213 - 1246
3X-RAY DIFFRACTION3A1247 - 1266
4X-RAY DIFFRACTION4A1267 - 1325
5X-RAY DIFFRACTION5A1326 - 1493
6X-RAY DIFFRACTION6B1175 - 1214
7X-RAY DIFFRACTION7B1215 - 1251
8X-RAY DIFFRACTION8B1252 - 1354
9X-RAY DIFFRACTION9B1355 - 1484
10X-RAY DIFFRACTION10B1485 - 1499

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