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- PDB-5yvx: Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide -

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Basic information

Entry
Database: PDB / ID: 5yvx
TitleCrystal structure of SDG8 CW domain in complex with H3K4me1 peptide
Components
  • H3K4me1
  • Histone-lysine N-methyltransferase ASHH2
KeywordsTRANSFERASE / SDG8 / CW domain / H3K4me1
Function / homology
Function and homology information


carotenoid metabolic process / response to nitrate starvation / : / anther development / regulation of plant-type hypersensitive response / negative regulation of flower development / plant ovule development / embryo sac development / secondary shoot formation / pollen development ...carotenoid metabolic process / response to nitrate starvation / : / anther development / regulation of plant-type hypersensitive response / negative regulation of flower development / plant ovule development / embryo sac development / secondary shoot formation / pollen development / : / chromocenter / regulation of programmed cell death / SUMO binding / histone H3K4 methyltransferase activity / plastid / chromosome, centromeric region / epigenetic regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Herpes Virus-1 - #100 / SETD2/Set2, SET domain / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains ...Herpes Virus-1 - #100 / SETD2/Set2, SET domain / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Herpes Virus-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 / Histone-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Histone-lysine N-methyltransferase ASHH2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.591 Å
AuthorsLiu, Y. / Huang, Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain ofArabidopsishistone methyltransferase SDG8.
Authors: Liu, Y. / Huang, Y.
History
DepositionNov 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase ASHH2
C: H3K4me1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0513
Polymers7,9862
Non-polymers651
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, the equilibrium disassociation constants (Kd) of SDG8 CW domain to H3K4me1 is 1.29 uM.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area4220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.421, 66.421, 29.241
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1173-

HOH

21C-105-

HOH

31C-108-

HOH

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Components

#1: Protein Histone-lysine N-methyltransferase ASHH2 / ASH1 homolog 2 / H3-K4-HMTase / Histone H3-K36 methyltransferase 8 / H3-K36-HMTase 8 / Protein ...ASH1 homolog 2 / H3-K4-HMTase / Histone H3-K36 methyltransferase 8 / H3-K36-HMTase 8 / Protein EARLY FLOWERING IN SHORT DAYS / Protein LAZARUS 2 / Protein SET DOMAIN GROUP 8


Mass: 6909.692 Da / Num. of mol.: 1 / Mutation: E917A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ASHH2, EFS, LAZ2, SDG8, SET8, At1g77300, T14N5.15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2LAE1, histone-lysine N-methyltransferase
#2: Protein/peptide H3K4me1 /


Mass: 1076.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P59226*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.5, 30% PEG 3350, 30% iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.2824 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 1.59→30 Å / Num. obs: 19136 / % possible obs: 98.6 % / Redundancy: 6.4 % / Net I/σ(I): 26.6
Reflection shellResolution: 1.59→1.65 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.591→28.761 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 17.87
RfactorNum. reflection% reflection
Rfree0.1845 1900 9.93 %
Rwork0.1675 --
obs0.1692 19132 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.591→28.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms529 0 1 84 614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007536
X-RAY DIFFRACTIONf_angle_d0.991718
X-RAY DIFFRACTIONf_dihedral_angle_d15.524199
X-RAY DIFFRACTIONf_chiral_restr0.04576
X-RAY DIFFRACTIONf_plane_restr0.00593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5913-1.63110.31911170.271103X-RAY DIFFRACTION87
1.6311-1.67520.26971320.24121222X-RAY DIFFRACTION98
1.6752-1.72450.24891440.23651240X-RAY DIFFRACTION99
1.7245-1.78010.23741360.20551198X-RAY DIFFRACTION99
1.7801-1.84370.2221430.18871279X-RAY DIFFRACTION100
1.8437-1.91750.20441260.18851247X-RAY DIFFRACTION100
1.9175-2.00480.2131400.1721226X-RAY DIFFRACTION100
2.0048-2.11040.1771350.16451240X-RAY DIFFRACTION100
2.1104-2.24260.20831420.17261249X-RAY DIFFRACTION100
2.2426-2.41570.20971410.16231236X-RAY DIFFRACTION100
2.4157-2.65860.17231390.17871254X-RAY DIFFRACTION100
2.6586-3.0430.16481360.18231243X-RAY DIFFRACTION100
3.043-3.83240.18381310.15011252X-RAY DIFFRACTION100
3.8324-28.76580.14821380.13791243X-RAY DIFFRACTION100

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