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Solution structure of the PHD1 domain of histone demethylase KDM5A
Authors
Longbotham, E.J., Kelly, M.J.S., Fujimori, D.G.
Assembly
Lysine-specific demethylase 5A (E.C.1.14.11.67)
Entity
1. Lysine-specific demethylase 5A (E.C.1.14.11.67), 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), entity ZN (non-polymer), 65.409 × 2 Da
Total weight
6730.322 Da
Max. entity weight
6599.504 Da
Entity Connection
na 8 Detail

IDTypeValue orderAtom ID 1Atom ID 2
1nasing1:CYS11:SG2:ZN1:ZN
2nasing1:CYS14:SG2:ZN1:ZN
3nasing1:HIS34:ND12:ZN1:ZN
4nasing1:CYS37:SG2:ZN1:ZN
5nasing1:CYS26:SG2:ZN1:ZN
6nasing1:CYS29:SG2:ZN1:ZN
7nasing1:CYS52:SG2:ZN1:ZN
8nasing1:CYS55:SG2:ZN1:ZN

Source organism
Homo sapiens
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 98.3 %, Completeness: 87.7 %, Completeness (bb): 81.4 % Detail

Polymer type: polypeptide(L)

Total1H13C15N
All87.7 % (585 of 667)94.5 % (326 of 345)78.6 % (206 of 262)88.3 % (53 of 60)
Backbone81.4 % (280 of 344)94.9 % (112 of 118)67.4 % (116 of 172)96.3 % (52 of 54)
Sidechain95.2 % (359 of 377)94.3 % (214 of 227)100.0 % (144 of 144)16.7 % (1 of 6)
Aromatic98.4 % (61 of 62)96.8 % (30 of 31)100.0 % (30 of 30)100.0 % (1 of 1)
Methyl100.0 % (52 of 52)100.0 % (26 of 26)100.0 % (26 of 26)

1. entity 1

GSVNFVDLYV CMFCGRGNNE DKLLLCDGCD DSYHTFCLIP PLPDVPKGDW RCPKCVAEE

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 900 uM U-13C, 99%; U-15N, 99 % PHD1, 50 mM HEPES, 150 mM NaCl, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
1PHD1[U-99% 13C; U-99% 15N]900 uM
2HEPESnatural abundance50 mM
3NaClnatural abundance150 mM
4beta-mercaptoethanolnatural abundance5 mM
5ZnCl2natural 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, 99%; U-15N, 99 % PHD1, 50 mM HEPES, 150 mM NaCl, 5 mM beta-mercaptoethanol, 0.1 mM ZnCl2, 95% H2O/5% D2O


#NameIsotope labelingTypeConcentration
6PHD1[U-99% 13C; U-99% 15N]550 uM
7HEPESnatural abundance50 mM
8NaClnatural abundance150 mM
9beta-mercaptoethanolnatural abundance5 mM
10ZnCl2natural abundance0.1 mM

Release date
2020-12-08
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: 30809 released on 2020-11-29
    Title Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide
Related entities 1. Lysine-specific demethylase 5A (E.C.1.14.11.67), entity 1, : 1 : 2 : 5 : 209 entities Detail
Interaction partners 1. Lysine-specific demethylase 5A (E.C.1.14.11.67), entity 1, : 13 interactors Detail
Experiments performed 8 experiments Detail
Chemical shift validation 4 contents Detail
Keywords Epigenetics, GENE REGULATION, H3, KDM5A, PHD