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- PDB-5vac: Crystal Structure of ATXR5 SET domain in complex with K36me3 hist... -

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Basic information

Entry
Database: PDB / ID: 5vac
TitleCrystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
Components
  • Histone H3.2
  • Probable Histone-lysine N-methyltransferase ATXR5
KeywordsTRANSFERASE/DNA BINDING PROTEIN / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / Chromatin modifying enzymes / histone acetyltransferase activity / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / chloroplast ...[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / Chromatin modifying enzymes / histone acetyltransferase activity / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / chloroplast / 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 / transcription coregulator activity / 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 / 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 / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / methylation / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger ...: / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Beta Complex / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Probable Histone-lysine N-methyltransferase ATXR5 / Histone H3.2
Similarity search - Component
Biological speciesRicinus communis (castor bean)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsBergamin, E. / Sarvan, S. / Malette, J. / Eram, M. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. ...Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.F.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Molecular basis for the methylation specificity of ATXR5 for histone H3.
Authors: Bergamin, E. / Sarvan, S. / Malette, J. / Eram, M.S. / Yeung, S. / Mongeon, V. / Joshi, M. / Brunzelle, J.S. / Michaels, S.D. / Blais, A. / Vedadi, M. / Couture, J.F.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable Histone-lysine N-methyltransferase ATXR5
C: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5554
Polymers28,0932
Non-polymers4632
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-6 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.548, 81.353, 88.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Probable Histone-lysine N-methyltransferase ATXR5


Mass: 26204.695 Da / Num. of mol.: 1 / Fragment: residues 146-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Gene: ATXR5, RCOM_1460410 / Production host: Escherichia coli (E. coli)
References: UniProt: B9RU15, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3.2 / Histone H3/m / Histone H3/o


Mass: 1888.239 Da / Num. of mol.: 1 / Fragment: residues 19-37 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71DI3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→55 Å / Num. obs: 18959 / % possible obs: 100 % / Redundancy: 7.6 % / Rsym value: 0.056 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O30

4o30


Resolution: 1.949→54.962 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2281 956 5.04 %
Rwork0.1888 --
obs0.1907 18959 94.72 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Bsol: 59.398 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.3958 Å2-0 Å20 Å2
2---11.865 Å2-0 Å2
3---1.4692 Å2
Refinement stepCycle: LAST / Resolution: 1.949→54.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 4 78 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071795
X-RAY DIFFRACTIONf_angle_d1.0632431
X-RAY DIFFRACTIONf_dihedral_angle_d14.603667
X-RAY DIFFRACTIONf_chiral_restr0.072272
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9493-2.05210.34911150.26572236X-RAY DIFFRACTION84
2.0521-2.18070.25841440.21252403X-RAY DIFFRACTION90
2.1807-2.34910.2231380.19492529X-RAY DIFFRACTION94
2.3491-2.58550.26381360.19042593X-RAY DIFFRACTION97
2.5855-2.95960.22641320.19512672X-RAY DIFFRACTION98
2.9596-3.72860.21581480.18512728X-RAY DIFFRACTION100
3.7286-54.98380.21071430.17592842X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.3681 Å / Origin y: -19.1116 Å / Origin z: -14.4757 Å
111213212223313233
T0.1882 Å2-0.0281 Å20.0336 Å2-0.1957 Å20.0024 Å2--0.199 Å2
L0.9657 °2-0.0217 °20.0487 °2-2.3705 °2-0.6 °2--1.7735 °2
S0.0214 Å °0.0278 Å °0.0033 Å °-0.0475 Å °0.065 Å °0.0146 Å °0.1181 Å °-0.0112 Å °-0.0724 Å °
Refinement TLS groupSelection details: all

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