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- PDB-5va6: CRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METH... -

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Basic information

Entry
Database: PDB / ID: 5va6
TitleCRYSTAL STRUCTURE OF ATXR5 IN COMPLEX WITH HISTONE H3.1 MONO-METHYLATED ON R26
Components
  • Histone H3.1Histone H3
  • Probable Histone-lysine N-methyltransferase ATXR5
KeywordsTRANSFERASE/DNA BINDING PROTEIN / nucleosome / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / chloroplast / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / chloroplast / 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 / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / transcription coregulator activity / 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 / PKMTs methylate histone lysines / RMTs methylate histone arginines / 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 / methylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / 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
Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / 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 H3.1
Similarity search - Component
Biological speciesRicinus communis (castor bean)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable Histone-lysine N-methyltransferase ATXR5
B: Probable Histone-lysine N-methyltransferase ATXR5
C: Histone H3.1
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7506
Polymers55,9824
Non-polymers7692
Water2,864159
1
A: Probable Histone-lysine N-methyltransferase ATXR5
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3753
Polymers27,9912
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area10830 Å2
MethodPISA
2
B: Probable Histone-lysine N-methyltransferase ATXR5
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3753
Polymers27,9912
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-7 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.310, 86.810, 74.040
Angle α, β, γ (deg.)90.00, 127.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26218.723 Da / Num. of mol.: 2 / 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 H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1772.078 Da / Num. of mol.: 2 / Fragment: residues 20-37 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 277 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: Mar 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→17 Å / Num. obs: 17859 / % possible obs: 96.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.061 / Net I/σ(I): 7.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O30

4o30


Resolution: 2.4→16.57 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.8661 / SU R Cruickshank DPI: 0.678 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.685 / SU Rfree Blow DPI: 0.331 / SU Rfree Cruickshank DPI: 0.335
RfactorNum. reflection% reflectionSelection details
Rfree0.297 922 5.16 %RANDOM
Rwork0.2457 ---
obs0.2485 17859 95.83 %-
Displacement parametersBiso mean: 35.32 Å2
Baniso -1Baniso -2Baniso -3
1-3.4156 Å20 Å210.9333 Å2
2---1.5256 Å20 Å2
3----1.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.422 Å
Refinement stepCycle: 1 / Resolution: 2.4→16.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 52 159 3692
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013617HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.234888HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1260SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes560HARMONIC5
X-RAY DIFFRACTIONt_it3617HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion19.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion487SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4114SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.6 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.4365 132 4.65 %
Rwork0.3558 2709 -
all0.3598 2841 -
obs--95.83 %
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)
11.48170.05240.45370.87440.02251.01970.0847-0.1089-0.08670.0536-0.0465-0.00410.08860.0168-0.0382-0.0882-0.00980.0819-0.13750.0196-0.145724.8428-17.64532.5359
21.40650.32250.6471.219-0.07341.80170.06460.02670.04170.1949-0.1099-0.0157-0.08920.02790.0453-0.04980.0150.0851-0.1828-0.0144-0.1643-0.8267-2.922930.0561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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