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- PDB-4ezh: the crystal structure of KDM6B bound with H3K27me3 peptide -

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Basic information

Entry
Database: PDB / ID: 4ezh
Titlethe crystal structure of KDM6B bound with H3K27me3 peptide
Components
  • Lysine-specific demethylase 6B
  • SYNTHESIZED methylation peptide
KeywordsOXIDOREDUCTASE / JmjC / histone demethylase / histone K27me3/me2 'eraser'
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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / response to fungicide / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / response to activity / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / hippocampus development / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / chromatin DNA binding / cellular response to hydrogen peroxide / PKMTs methylate histone lysines / RMTs methylate histone arginines / beta-catenin binding / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromatin remodeling / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ribbon / Histone-fold / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Histone H3.1 / Lysine-specific demethylase 6B
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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

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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
C: SYNTHESIZED methylation peptide
D: SYNTHESIZED methylation peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,37510
Polymers111,8324
Non-polymers5426
Water1,47782
1
A: Lysine-specific demethylase 6B
C: SYNTHESIZED methylation peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1875
Polymers55,9162
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-17 kcal/mol
Surface area21380 Å2
MethodPISA
2
B: Lysine-specific demethylase 6B
D: SYNTHESIZED methylation peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1875
Polymers55,9162
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-16 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.682, 102.413, 143.200
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

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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: Protein/peptide SYNTHESIZED methylation peptide


Mass: 1030.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THIS SEQUENCE WAS SYNTHESIZED BY TUFTS UNIVERSITY / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS

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Non-polymers , 4 types, 88 molecules

#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: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 293 K / pH: 8.2
Details: 11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES 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-C / Wavelength: 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 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: 2.5→40 Å / Num. obs: 41888 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 7 % / Rmerge(I) obs: 0.111 / Rsym value: 0.072
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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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: 2.52→40 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 35.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 2105 5.05 %
Rwork0.213 --
obs0.215 41687 98.7 %
all-41888 -
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.64 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.5876 Å20 Å20 Å2
2--9.3638 Å20 Å2
3---0.2238 Å2
Refinement stepCycle: LAST / Resolution: 2.52→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7429 0 24 82 7535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197656
X-RAY DIFFRACTIONf_angle_d1.46610420
X-RAY DIFFRACTIONf_dihedral_angle_d17.3542770
X-RAY DIFFRACTIONf_chiral_restr0.0881138
X-RAY DIFFRACTIONf_plane_restr0.0061330
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2609X-RAY DIFFRACTIONPOSITIONAL
12B2609X-RAY DIFFRACTIONPOSITIONAL0.166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5209-2.57950.52391030.412254X-RAY DIFFRACTION85
2.5795-2.6440.38261530.36692624X-RAY DIFFRACTION99
2.644-2.71550.36291550.32132605X-RAY DIFFRACTION99
2.7155-2.79540.34931230.28652623X-RAY DIFFRACTION99
2.7954-2.88560.31931400.26712646X-RAY DIFFRACTION100
2.8856-2.98870.31851480.24072627X-RAY DIFFRACTION100
2.9887-3.10830.27971430.23092635X-RAY DIFFRACTION100
3.1083-3.24970.28261320.22682662X-RAY DIFFRACTION100
3.2497-3.4210.24741530.21732634X-RAY DIFFRACTION100
3.421-3.63520.28491480.20562638X-RAY DIFFRACTION100
3.6352-3.91560.23171260.19482680X-RAY DIFFRACTION100
3.9156-4.30930.24821490.17342684X-RAY DIFFRACTION100
4.3093-4.93190.19121350.15612716X-RAY DIFFRACTION100
4.9319-6.20990.22161320.22731X-RAY DIFFRACTION100
6.2099-40.16680.20561650.19372823X-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)
11.2589-0.69450.27731.546-0.44182.07530.00170.0397-0.256-0.220.16830.25410.2128-0.2668-0.18460.4628-0.1276-0.00070.6426-0.03680.1551-3.6211-8.1688-40.6247
21.182-1.10230.55521.6919-0.75761.72150.09960.05080.1797-0.2631-0.1355-0.2477-0.08370.6603-0.01880.4765-0.1486-0.00650.70490.07940.160718.90853.3399-48.5301
31.56840.46030.69491.91370.42592.3804-0.14130.31160.103-0.30980.17820.0172-0.3750.2454-0.04480.5269-0.3021-0.03130.44110.00950.25826.795516.2399-56.4486
41.16730.1207-0.27581.0318-0.73583.94980.0929-0.35490.21660.1335-0.06230.0378-0.57670.0892-0.03050.36310.02150.01580.429-0.03840.1387-3.56359.7241-41.2659
50.6891-0.3556-0.14380.5981-0.27931.5144-0.0014-0.20560.00760.06490.05050.03660.06620.06430.07360.2635-0.12420.00590.54080.0053-0.28885.8683-3.7505-37.7833
61.57930.04730.4431.59011.03634.40130.0786-0.33770.31740.1095-0.0401-0.1567-0.20480.37380.05390.3715-0.14070.00010.8370.010.2253.6037-0.938-9.1642
70.9353-0.090.05311.1482-0.63941.857-0.0506-0.09520.12520.13270.14060.1116-0.1371-0.1648-0.18720.4183-0.07750.07490.8535-0.04840.1874-38.69770.3892-17.6167
80.73890.1468-0.2030.7903-0.02931.7733-0.0234-0.0320.09260.01480.05460.0730.0136-0.1081-0.030.3728-0.09490.03450.8049-0.00140.1997-37.74011.2749-24.5593
90.8724-0.7739-0.39991.71640.82844.49490.05970.2304-0.0359-0.0169-0.07940.0340.04790.13750.07140.3127-0.0725-0.00090.81420.08820.2455-38.33230.9335-53.7504
100.00090.0004-0.00010.0005-0.0010.00120.00470.0034-0.0111-0.0011-0.0122-0.01030.01130.0008-00.5693-0.12140.00280.6554-0.00070.474310.85698.5996-33.9119
110.0007-0.0001-0.0004-0.000700.0017-0.01260.0008-0.00140.0076-0.0318-0.0187-0.01550.003200.58490.0890.07910.7304-0.11230.508-30.9629-8.5143-28.9125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1157:1239 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 1240:1268 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1269:1298 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1299:1352 )
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1353:1503 )
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1504:1636 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 1157:1297 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 1298:1503 )
9X-RAY DIFFRACTION9(CHAIN B AND RESID 1504:1638 )

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