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Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide
Authors
Longbotham, E.J., Kelly, M.J.S., Fujimori, D.G.
Assembly
Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1
Entity
1. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 1 (polymer, Thiol state: all other bound), 59 monomers, 6599.504 Da Detail

GSVNFVDLYV CMFCGRGNNE DKLLLCDGCD DSYHTFCLIP PLPDVPKGDW RCPKCVAEE


2. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 2 (polymer, Thiol state: not present), 10 monomers, 1146.300 Da Detail

ARTKQTARKS


3. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity ZN (non-polymer), 65.409 × 2 Da
Total weight
7876.6216 Da
Max. entity weight
6599.504 Da
Entity Connection
disulfide 8 Detail

IDTypeValue orderAtom ID 1Atom ID 2
1disulfidesing1:CYS11:SG3:ZN1:ZN
2disulfidesing1:CYS14:SG3:ZN1:ZN
3disulfidesing1:CYS26:SG3:ZN1:ZN
4disulfidesing1:CYS29:SG3:ZN1:ZN
5disulfidesing1:HIS34:ND13:ZN1:ZN
6disulfidesing1:CYS37:SG3:ZN1:ZN
7disulfidesing1:CYS52:SG3:ZN1:ZN
8disulfidesing1:CYS55:SG3:ZN1:ZN

Source organism
Homo sapiens
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 98.6 %, Completeness: 82.0 %, Completeness (bb): 74.0 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All82.0 % (645 of 787)94.9 % (388 of 409)66.9 % (204 of 305)72.6 % (53 of 73)
Backbone74.0 % (299 of 404)95.7 % (132 of 138)56.9 % (115 of 202)81.3 % (52 of 64)
Sidechain89.5 % (400 of 447)94.5 % (256 of 271)85.6 % (143 of 167)11.1 % (1 of 9)
Aromatic96.8 % (60 of 62)96.8 % (30 of 31)96.7 % (29 of 30)100.0 % (1 of 1)
Methyl93.3 % (56 of 60)100.0 % (30 of 30)86.7 % (26 of 30)

1. entity 1

GSVNFVDLYV CMFCGRGNNE DKLLLCDGCD DSYHTFCLIP PLPDVPKGDW RCPKCVAEE

2. entity 2

ARTKQTARKS

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 900 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 4000 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1Histone lysine demethylase 5A, KDM5A[U-13C; U-15N]900 uM
2Histone H3.1natural abundance4000 uM
3HEPESnatural abundance50 mM
4sodium chloridenatural abundance150 mM
5beta-mercaptoethanolnatural abundance5 mM
6ZnCl2natural abundance0.1 mM
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 550 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 800 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
7Histone lysine demethylase 5A, KDM5A[U-13C; U-15N]550 uM
8Histone H3.1natural abundance800 uM
9HEPESnatural abundance50 mM
10sodium chloridenatural abundance150 mM
11beta-mercaptoethanolnatural abundance5 mM
12ZnCl2natural abundance0.1 mM
Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1250 uM [U-13C; U-15N] Histone lysine demethylase 5A, KDM5A, 400 uM Histone H3.1, 50 mM HEPES, 150 mM sodium chloride, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
13Histone lysine demethylase 5A, KDM5A[U-13C; U-15N]1250 uM
14Histone H3.1natural abundance400 uM
15HEPESnatural abundance50 mM
16sodium chloridenatural abundance150 mM
17beta-mercaptoethanolnatural abundance5 mM
18ZnCl2natural abundance0.1 mM

Release date
2020-11-29
Citation
Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A
Longbotham, J.E., Kelly, M.J.S., Fujimori, D.G.
ACS Chem. Biol. (2021), PubMed 33621062 , DOI 10.1021/acschembio.0c00976 ,
Entries sharing articles BMRB: 1 entries Detail
  BMRB: 30808 released on 2020-12-08
    Title Solution structure of the PHD1 domain of histone demethylase KDM5A
Related entities 1. Lysine-specific demethylase 5A (E.C.1.14.11.67), Histone H3.1, entity 1, : 1 : 2 : 5 : 209 entities Detail
Experiments performed 11 experiments Detail
Chemical shift validation 5 contents Detail
Keywords Epigenetics, GENE REGULATION, H3, KDM5A, PHD