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- PDB-5vbc: Crystal structure of ATXR5 in complex with histone H3.1 -

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Basic information

Entry
Database: PDB / ID: 5vbc
TitleCrystal structure of ATXR5 in complex with histone H3.1
Components
  • Histone H3.1 peptide
  • Probable Histone-lysine N-methyltransferase ATXR5
KeywordsTRANSFERASE/DNA BINDING PROTEIN / nucleosome / methylation / 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: 2.1 Å
AuthorsCouture, J.-F. / Bergamin, E.
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 29, 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

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 peptide
D: Histone H3.1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0327
Polymers55,1854
Non-polymers8473
Water5,170287
1
A: Probable Histone-lysine N-methyltransferase ATXR5
C: Histone H3.1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0554
Polymers27,5922
Non-polymers4632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-7 kcal/mol
Surface area10570 Å2
MethodPISA
2
B: Probable Histone-lysine N-methyltransferase ATXR5
D: Histone H3.1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9773
Polymers27,5922
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-6 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.170, 87.310, 74.510
Angle α, β, γ (deg.)90.00, 127.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26246.797 Da / Num. of mol.: 2 / Fragment: SET domain 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 peptide / Histone H3.2


Mass: 1345.590 Da / Num. of mol.: 2 / Fragment: residues 24-37 / 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: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50% polypropylene glycol 400, 100mM Na-Hepes pH 6.0 and 5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→27 Å / Num. obs: 29410 / % possible obs: 98.3 % / Redundancy: 4.1 % / Rsym value: 0.06 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4o30

4o30


Resolution: 2.1→26.404 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.49 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2344 1493 5.08 %
Rwork0.1961 --
obs0.1981 29390 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 56 287 3880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083675
X-RAY DIFFRACTIONf_angle_d0.9974958
X-RAY DIFFRACTIONf_dihedral_angle_d15.2082263
X-RAY DIFFRACTIONf_chiral_restr0.056544
X-RAY DIFFRACTIONf_plane_restr0.005651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.31471410.23782457X-RAY DIFFRACTION96
2.1678-2.24520.28251480.22862488X-RAY DIFFRACTION97
2.2452-2.3350.28021310.21952480X-RAY DIFFRACTION97
2.335-2.44120.33131390.21632525X-RAY DIFFRACTION98
2.4412-2.56980.24121290.21882538X-RAY DIFFRACTION98
2.5698-2.73070.30061200.22212538X-RAY DIFFRACTION98
2.7307-2.94130.26871420.21212533X-RAY DIFFRACTION99
2.9413-3.23680.25681200.2122579X-RAY DIFFRACTION99
3.2368-3.70410.20991420.18992571X-RAY DIFFRACTION99
3.7041-4.66260.18161270.15832583X-RAY DIFFRACTION100
4.6626-26.40630.21751540.1952605X-RAY DIFFRACTION99

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