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- PDB-5vah: Crystal structure of ATXR5 SET domain in complex with histone H3 ... -

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Basic information

Entry
Database: PDB / ID: 5vah
TitleCrystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26
Components
  • Histone H3.2
  • Probable Histone-lysine N-methyltransferase ATXR5
KeywordsTRANSFERASE/DNA BINDING PROTEIN / histone / nucleosome / methyltransferases / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / chromocenter / plastid / chloroplast / transcription coregulator activity / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity ...[histone H3]-lysine27 N-methyltransferase / histone H3K27 monomethyltransferase activity / chromocenter / plastid / chloroplast / transcription coregulator activity / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
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)
Arabidopsis thaliana (thale cress)
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 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,0386
Polymers55,2694
Non-polymers7692
Water3,063170
1
A: Probable Histone-lysine N-methyltransferase ATXR5
C: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0193
Polymers27,6342
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-7 kcal/mol
Surface area9810 Å2
MethodPISA
2
B: Probable Histone-lysine N-methyltransferase ATXR5
D: Histone H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0193
Polymers27,6342
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-8 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.201, 87.188, 74.022
Angle α, β, γ (deg.)90.00, 127.87, 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 H3.2 / Histone H3.1


Mass: 1415.637 Da / Num. of mol.: 2 / Fragment: residues 22-36 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226
#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.: 170 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting 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 16, 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: 19507 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.13 Å2 / Rsym value: 0.061 / Net I/σ(I): 3.5

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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→16.93 Å / Cor.coef. Fo:Fc: 0.9112 / Cor.coef. Fo:Fc free: 0.8798 / SU R Cruickshank DPI: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.475 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.2806 995 5.1 %RANDOM
Rwork0.2279 ---
obs0.2305 19507 98.07 %-
Displacement parametersBiso mean: 37.14 Å2
Baniso -1Baniso -2Baniso -3
1-3.5969 Å20 Å27.7453 Å2
2---6.8231 Å20 Å2
3---3.2262 Å2
Refine analyzeLuzzati coordinate error obs: 0.332 Å
Refinement stepCycle: 1 / Resolution: 2.4→16.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 52 170 3625
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144781HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1200SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes551HARMONIC5
X-RAY DIFFRACTIONt_it3527HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion18.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion480SEMIHARMONIC5
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_contact4028SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3648 134 4.63 %
Rwork0.2636 2758 -
all0.2681 2892 -
obs--98.07 %

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