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- PDB-3avr: Catalytic fragment of UTX/KDM6A bound with histone H3K27me3 pepti... -

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Basic information

Entry
Database: PDB / ID: 3avr
TitleCatalytic fragment of UTX/KDM6A bound with histone H3K27me3 peptide, N-oxyalylglycine, and Ni(II)
Components
  • Histone H3
  • Lysine-specific demethylase 6A
KeywordsOXIDOREDUCTASE/STRUCTURAL PROTEIN / Cupin superfamily / tri/dimethyllysine demethylase / OXIDOREDUCTASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / histone demethylase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening ...[histone H3]-trimethyl-L-lysine27 demethylase / histone H3K27me2/H3K27me3 demethylase activity / MLL3/4 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / histone demethylase activity / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / chromatin DNA binding / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Tetratricopeptide repeat ...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 / Tetratricopeptide repeat / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 6A / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsSengoku, T. / Yokoyama, S.
CitationJournal: Genes Dev. / Year: 2011
Title: Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A
Authors: Sengoku, T. / Yokoyama, S.
History
DepositionMar 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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 6A
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,47916
Polymers62,5782
Non-polymers90114
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-8 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.905, 83.081, 95.057
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 / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Lysine-specific demethylase 6A / Histone demethylase UTX / Ubiquitously-transcribed TPR protein on the X chromosome / Ubiquitously- ...Histone demethylase UTX / Ubiquitously-transcribed TPR protein on the X chromosome / Ubiquitously-transcribed X chromosome tetratricopeptide repeat protein


Mass: 60264.375 Da / Num. of mol.: 1 / Fragment: UNP residues 880-1401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM6A, UTX / Plasmid: pET47 / Production host: Escherichia coli (E. coli)
References: UniProt: O15550, 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 Histone H3


Mass: 2313.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis / References: UniProt: P68431*PLUS

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Non-polymers , 6 types, 402 molecules

#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl (pH 8.5), 0.2M Li2SO4, 18-20% PEG 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 29, 2010
RadiationMonochromator: Double Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 58666 / Num. obs: 58138 / % possible obs: 99.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.8→1.86 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AVS

3avs


Resolution: 1.803→30.357 Å / FOM work R set: 0.8734 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 2979 5.13 %RANDOM
Rwork0.1694 ---
obs0.1709 58029 --
all-58666 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.988 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2948 Å20 Å2-0 Å2
2--0.124 Å2-0 Å2
3----4.6761 Å2
Refinement stepCycle: LAST / Resolution: 1.803→30.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 50 388 4358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074129
X-RAY DIFFRACTIONf_angle_d1.1015610
X-RAY DIFFRACTIONf_dihedral_angle_d13.7771540
X-RAY DIFFRACTIONf_chiral_restr0.073607
X-RAY DIFFRACTIONf_plane_restr0.005724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8031-1.86750.34442770.2771528197
1.8675-1.94230.24433110.22045458100
1.9423-2.03060.23533060.18815431100
2.0306-2.13770.23262880.16855471100
2.1377-2.27160.18262970.15515448100
2.2716-2.44690.17992860.1525516100
2.4469-2.6930.19823050.15925522100
2.693-3.08230.20852970.16825548100
3.0823-3.88220.2013120.17345561100
3.8822-30.3610.16483000.15815814100
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)
10.6993-0.3698-0.45210.28210.15330.37530.2274-0.00870.1142-0.0893-0.2281-0.1003-0.0493-0.02150.01440.3111-0.0764-0.00920.25280.00420.18827.95329.2656-12.376
20.50660.2577-0.00451.09080.28111.1371-0.016-0.0146-0.01360.0091-0.02770.04570.0756-0.12780.0310.1409-0.01130.01910.15590.00890.1367-16.1254-9.3398-15.045
30.24770.1557-0.21450.6474-0.0060.26110.04-0.10310.01180.2216-0.0103-0.1080.1012-0.005-0.01870.2113-0.0151-0.02780.19340.02550.1464-7.1946-8.4648-4.4716
40.31920.3782-0.00260.62740.09470.51340.0085-0.01370.011-0.0126-0.03130.023-0.0219-0.05210.02040.1259-0.00130.01170.1326-00.1382-13.11250.4818-15.8782
50.2706-0.2418-0.04330.64430.44170.44620.1095-0.03130.08620.0517-0.14480.0081-0.20620.09060.01790.247-0.07790.03750.1549-0.00160.18643.87822.558-8.4686
60.27030.19390.15740.6125-0.12880.20490.1983-0.2022-0.02790.3667-0.1676-0.0258-0.15550.1597-0.00720.3036-0.11480.05260.2517-0.03620.1341-2.174619.5764.5763
70.0626-0.0046-0.00650.0165-0.01170.0099-0.0871-0.0149-0.02910.0708-0.080.02510.0001-0.01140.14280.6635-0.06590.09390.5669-0.00890.2979-4.22814.017914.2082
80.2897-0.03660.4120.0532-0.02780.60250.3498-0.20870.09160.1286-0.0393-0.0573-0.10240.0693-0.22410.265-0.04250.07240.2791-0.05310.2002-16.97342.212-1.9338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 886:918)
2X-RAY DIFFRACTION2chain 'A' and (resseq 919:1046)
3X-RAY DIFFRACTION3chain 'A' and (resseq 1047:1132)
4X-RAY DIFFRACTION4chain 'A' and (resseq 1133:1285)
5X-RAY DIFFRACTION5chain 'A' and (resseq 1286:1312)
6X-RAY DIFFRACTION6chain 'A' and (resseq 1313:1395)
7X-RAY DIFFRACTION7chain 'B' and (resseq 17:21)
8X-RAY DIFFRACTION8chain 'B' and (resseq 22:33)

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