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- PDB-4eyu: The free structure of the mouse C-terminal domain of KDM6B -

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Basic information

Entry
Database: PDB / ID: 4eyu
TitleThe free structure of the mouse C-terminal domain of KDM6B
ComponentsLysine-specific demethylase 6B
KeywordsOXIDOREDUCTASE / JMJC domain / Histone K27 trimethyl and dimethyl demethylase
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / HDMs demethylate histones / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / Oxidative Stress Induced Senescence / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / cell fate commitment ...[histone H3]-trimethyl-L-lysine27 demethylase / HDMs demethylate histones / histone H3K27me2/H3K27me3 demethylase activity / endothelial cell differentiation / Oxidative Stress Induced Senescence / cardiac muscle cell differentiation / MLL3/4 complex / mesodermal cell differentiation / inflammatory response to antigenic stimulus / cell fate commitment / response to fungicide / response to activity / hippocampus development / chromatin DNA binding / beta-catenin binding / cellular response to hydrogen peroxide / positive regulation of cold-induced thermogenesis / regulation of gene expression / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
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
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 6B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheng, Z.J. / Patel, D.J.
CitationJournal: Nature / Year: 2012
Title: A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.
Authors: Kruidenier, L. / Chung, C.W. / 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.W. / 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
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen ...audit_author / entity_src_gen / pdbx_entity_src_syn / software
Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_asym_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_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.value / _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_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)110,3148
Polymers109,7722
Non-polymers5426
Water3,207178
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A: Lysine-specific demethylase 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1574
Polymers54,8861
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1574
Polymers54,8861
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.977, 102.284, 145.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1155:1168 or resseq 1321:1565 or resseq...
211chain B and (resseq 1155:1168 or resseq 1321:1565 or resseq...

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Components

#1: Protein Lysine-specific demethylase 6B / JmjC domain-containing protein 3 / Jumonji domain-containing protein 3


Mass: 54885.965 Da / Num. of mol.: 2 / Fragment: UNP residues 1155-1641
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kdm6b, Jmjd3, Kiaa0346 / Plasmid: PET28 SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5NCY0, 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: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREPLACEMENT OF THE ORIGINAL LOOP SEQUENCE OF ESEDEESEEPDSTTGTSPSSAPDPKN(RESIDUES 1296-1322) WITH ...REPLACEMENT OF THE ORIGINAL LOOP SEQUENCE OF ESEDEESEEPDSTTGTSPSSAPDPKN(RESIDUES 1296-1322) WITH RESIDUES OF LEVLFQGPTKAARKSAPATGGGSSGS.

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 298 K / pH: 8.2
Details: 11% methanol, 6% MPD, 5% PEG 4K, 5% GLYCEROL, HEPES pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2011 / Details: SI MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 55090 / % possible obs: 99.3 % / Observed criterion σ(I): 1.8 / Redundancy: 7 % / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.45 Å / SU ML: 0.65 / σ(F): 1.34 / Phase error: 37.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2767 5.05 %
Rwork0.23 --
obs0.232 54823 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.41 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.2897 Å20 Å2-0 Å2
2--36.0011 Å2-0 Å2
3----16.7114 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7309 0 24 178 7511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127518
X-RAY DIFFRACTIONf_angle_d1.14510240
X-RAY DIFFRACTIONf_dihedral_angle_d15.2582722
X-RAY DIFFRACTIONf_chiral_restr0.0681118
X-RAY DIFFRACTIONf_plane_restr0.0061310
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2609X-RAY DIFFRACTIONPOSITIONAL
12B2609X-RAY DIFFRACTIONPOSITIONAL0.064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2971-2.33670.42041200.3892159X-RAY DIFFRACTION83
2.3367-2.37920.4771200.38592523X-RAY DIFFRACTION96
2.3792-2.42490.34841450.37482543X-RAY DIFFRACTION97
2.4249-2.47440.42571270.34982525X-RAY DIFFRACTION97
2.4744-2.52820.37681390.34352568X-RAY DIFFRACTION97
2.5282-2.5870.36961390.31932588X-RAY DIFFRACTION99
2.587-2.65170.32341540.29182588X-RAY DIFFRACTION100
2.6517-2.72340.34591470.28212601X-RAY DIFFRACTION99
2.7234-2.80350.39971470.27232603X-RAY DIFFRACTION99
2.8035-2.89390.26811440.2542613X-RAY DIFFRACTION100
2.8939-2.99730.29891460.23932630X-RAY DIFFRACTION99
2.9973-3.11730.28281340.23542628X-RAY DIFFRACTION100
3.1173-3.25910.25481270.23252633X-RAY DIFFRACTION100
3.2591-3.43080.26561170.21512666X-RAY DIFFRACTION100
3.4308-3.64560.24751600.21432635X-RAY DIFFRACTION99
3.6456-3.92680.22821240.19812672X-RAY DIFFRACTION100
3.9268-4.32150.23991380.17322655X-RAY DIFFRACTION100
4.3215-4.94570.19371380.15982687X-RAY DIFFRACTION100
4.9457-6.22680.21041460.20592723X-RAY DIFFRACTION100
6.2268-38.45150.20261550.19042816X-RAY DIFFRACTION99
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)
12.355-1.01110.19511.3153-0.5610.6983-0.11590.0221-0.5512-0.13360.26210.1790.52920.034-0.16110.5305-0.1472-0.02670.6287-0.0230.4653-1.3459-16.3905-38.2808
22.8198-1.37140.35582.3912-1.30283.45270.01380.0762-0.0523-0.20320.14660.1402-0.2268-0.5851-0.17860.3752-0.12920.02690.65430.03430.2649-7.14033.383-45.0236
32.2516-1.57760.36921.5777-0.99771.84710.17380.20660.4868-0.2852-0.1589-0.4517-0.21930.80540.05370.4038-0.22180.03970.7796-0.01990.385518.8462.9059-49.6284
41.3450.70840.17821.8283-0.09650.614-0.08010.33620.2094-0.29330.25950.0221-0.36990.21940.15020.696-0.41750.04690.04580.01630.45326.851815.847-57.6518
50.6243-0.47380.31610.7565-0.83314.30450.009-0.43830.02930.1337-0.04380.0394-0.5177-0.0488-0.07120.3411-0.06270.02210.4115-0.06210.2908-4.03737.2739-36.8056
62.034-1.0416-0.05091.0145-0.64872.5577-0.0504-0.14420.00830.03970.0218-0.0350.080.1725-0.03750.2795-0.1466-0.01220.3571-0.01520.27117.5085-4.8284-40.0428
72.24780.44970.4121.73191.26714.97190.0856-0.44590.23020.1037-0.1567-0.0537-0.08860.35660.04380.3356-0.1539-0.01270.83430.03140.35213.5763-0.6588-9.434
81.2567-0.7169-0.10781.958-0.98562.197-0.0653-0.13810.34740.16970.2432-0.129-0.3963-0.0546-0.2020.5059-0.2240.0230.8726-0.14680.49-42.007816.2392-25.9582
91.7584-0.07803.935-1.53681.7330.0681-0.1750.18830.31320.26030.2217-0.0823-0.7608-0.43590.3906-0.10450.04811.04350.03010.3614-50.36086.0706-21.3539
103.46890.99320.652.4183-0.90132.61380.0723-0.1643-0.34-0.01130.0928-0.09180.30570.0538-0.20550.3807-0.06670.02930.8189-0.06920.3502-32.5985-10.4239-15.8928
112.27410.79870.30593.3678-1.37671.7183-0.0289-0.2509-0.12920.2230.2295-0.1683-0.01830.2401-0.10820.3566-0.0590.02430.8297-0.07580.335-29.8327-11.1757-10.0358
121.3706-0.9401-0.44752.0998-1.64094.2343-0.12820.1625-0.0618-0.01720.14570.13440.451-0.26630.00030.4392-0.28640.00830.8998-0.04530.4244-45.5031-7.4093-27.4982
131.4263-0.13380.61890.9361-0.57832.556-0.0448-0.08780.123-0.01530.1189-0.0672-0.1524-0.0874-0.03450.3581-0.1530.02640.8227-0.06870.3876-34.01494.7673-24.3472
141.7458-1.4751-0.65951.59811.44124.40830.11550.3008-0.0876-0.05-0.147-0.0444-0.09680.26620.0750.3128-0.1538-0.00070.72770.0770.3697-38.32051.7006-53.2272
150.31060.4680.2551.03230.29763.5064-0.09660.1133-0.210.0809-0.009-0.06830.37290.29210.00520.341-0.06920.0290.88570.10390.3445-37.3771-1.5586-58.1316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1157:1203 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1204:1239 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1240:1268 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1269:1298 )
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1299:1374 )
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1375:1503 )
7X-RAY DIFFRACTION7(CHAIN A AND RESID 1504:1636 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1157:1196 )
9X-RAY DIFFRACTION9(CHAIN B AND RESID 1197:1228 )
10X-RAY DIFFRACTION10(CHAIN B AND RESID 1229:1257 )
11X-RAY DIFFRACTION11(CHAIN B AND RESID 1258:1297 )
12X-RAY DIFFRACTION12(CHAIN B AND RESID 1298:1374 )
13X-RAY DIFFRACTION13(CHAIN B AND RESID 1375:1503 )
14X-RAY DIFFRACTION14(CHAIN B AND RESID 1504:1589 )
15X-RAY DIFFRACTION15(CHAIN B AND RESID 1594:1638 )

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