- PDB-5yvx: Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide -
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Entry
Database: PDB / ID: 5yvx
Title
Crystal structure of SDG8 CW domain in complex with H3K4me1 peptide
Components
H3K4me1
Histone-lysine N-methyltransferase ASHH2
Keywords
TRANSFERASE / 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 / regulation of programmed cell death ...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 / regulation of programmed cell death / chromocenter / SUMO binding / histone H3K4 methyltransferase activity / plastid / chromosome, centromeric region / Transferases; Transferring one-carbon groups; Methyltransferases / epigenetic regulation of gene expression / structural constituent of chromatin / nucleosome / methylation / protein heterodimerization activity / DNA binding / extracellular region / zinc ion binding / 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 ...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 / Herpes Virus-1 / SET domain superfamily / SET domain profile. / SET domain / 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
Journal: 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.
Evidence: isothermal titration calorimetry, the equilibrium disassociation constants (Kd) of SDG8 CW domain to H3K4me1 is 1.29 uM.
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
Buried area
1130 Å2
ΔGint
-9 kcal/mol
Surface area
4220 Å2
Method
PISA
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 number
173
Space group name H-M
P63
Components on special symmetry positions
ID
Model
Components
1
1
A-1173-
HOH
2
1
C-105-
HOH
3
1
C-108-
HOH
-
Components
#1: Protein
Histone-lysineN-methyltransferaseASHH2 / 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
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