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Basic information

Entry
Database: PDB / ID: 4ez4
Titlefree KDM6B structure
ComponentsLysine-specific demethylase 6B
KeywordsOXIDOREDUCTASE / mjd3/KDM6B / JmjC domain / histone 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 / cellular response to hydrogen peroxide / beta-catenin binding / 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: 2.99 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 2, 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 / Category: entity_src_gen / pdbx_entity_src_syn / software
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
Water21612
1
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)57.660, 123.707, 82.043
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211
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 1173:1287 or resseq...
211chain B and (resseq 1155:1168 or resseq 1173:1287 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, EC: 1.14.112
#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.: 12 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 293 K / pH: 8.2
Details: 11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: SI MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. all: 21929 / Num. obs: 20977 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.119 / Rsym value: 0.132
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.294 / % possible all: 91.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→49.73 Å / SU ML: 0.76 / σ(F): 1.44 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1079 5.15 %
Rwork0.19 --
obs0.193 20961 95.6 %
all-21880 -
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.03 Å2 / ksol: 0.27 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.603 Å2-0 Å2-7.4613 Å2
2---15.4791 Å20 Å2
3---1.8761 Å2
Refinement stepCycle: LAST / Resolution: 2.99→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7186 0 24 12 7222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167397
X-RAY DIFFRACTIONf_angle_d1.67910077
X-RAY DIFFRACTIONf_dihedral_angle_d19.3732683
X-RAY DIFFRACTIONf_chiral_restr0.1031100
X-RAY DIFFRACTIONf_plane_restr0.0091289
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3529X-RAY DIFFRACTIONPOSITIONAL
12B3529X-RAY DIFFRACTIONPOSITIONAL0.111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9932-3.12940.26781080.22242344X-RAY DIFFRACTION90
3.1294-3.29440.31831470.222408X-RAY DIFFRACTION93
3.2944-3.50070.28531390.21412462X-RAY DIFFRACTION96
3.5007-3.77090.23221260.17722532X-RAY DIFFRACTION96
3.7709-4.15020.21831200.16222515X-RAY DIFFRACTION97
4.1502-4.75040.21651180.14952535X-RAY DIFFRACTION97
4.7504-5.98330.24351530.19182534X-RAY DIFFRACTION98
5.9833-49.73620.2541680.21332552X-RAY DIFFRACTION98
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)
11.8607-0.38370.12540.84310.09891.12660.19950.2181-0.27920.0306-0.19250.05660.4067-0.11580.10280.3025-0.08630.03220.2936-0.02380.16924.5977-25.186121.9947
20.68770.1663-1.51750.884-0.49693.3692-0.14530.54110.44730.20180.0412-0.07570.18590.49070.2920.4215-0.1381-0.10130.54590.06070.402227.9754-22.83534.1173
31.58311.7984-0.03493.94260.19434.9829-0.50370.2973-0.10470.08310.0079-0.99190.46840.7196-0.30550.25260.1050.04290.67090.08040.374235.1587-20.799619.9924
40.8224-0.39210.03440.74220.00071.17730.10270.23960.09870.0757-0.1201-0.0222-0.00480.0780.10480.10540.02210.08130.35020.0702-0.039613.8359-19.165626.0789
51.6002-0.60250.40851.3707-0.33121.6347-0.1043-0.11310.41510.2293-0.07670.0595-0.4027-0.2058-0.03370.1876-0.0694-0.07830.3610.07290.04950.89641.207831.2508
61.1581-0.2901-0.5320.6640.39560.96460.2160.04930.0968-0.1025-0.20940.0262-0.2624-0.2478-0.12760.1968-0.06920.03830.38830.06440.2395-6.2565-0.3311-17.2195
70.88060.15770.11761.46060.12911.5181-0.137-0.1103-0.03690.14890.05390.4183-0.0262-0.30330.00240.12730.01440.09820.40850.0460.2312-17.74840.24314.2612
81.1511-0.6757-0.08181.19280.5760.934-0.0027-0.044-0.1686-0.1724-0.10180.1247-0.0425-0.1614-0.00870.0319-0.0535-0.09790.3584-0.04980.0445-5.2172-6.93-11.2229
91.41470.0803-0.31692.88-0.73432.99540.0450.0331-0.2526-0.32080.1016-0.05661.01860.0865-0.01330.4173-0.02960.00390.33850.05590.21248.2853-32.3226-15.3182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1157:1235 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1236:1268 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1269:1292 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1293:1466 )
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1467:1636 )
6X-RAY DIFFRACTION6(CHAIN B AND RESID 1157:1247 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1248:1291 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1292:1527 )
9X-RAY DIFFRACTION9(CHAIN B AND RESID 1528:1638 )

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