BMRB Entry 30809

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30809
MolProbity Validation Chart

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Title:
Solution structure of the PHD1 domain of histone demethylase KDM5A in complex with a histone H3(1-10) peptide
Deposition date:
2020-10-31
Original release date:
2021-03-01
Authors:
Longbotham, E.; Kelly, M.; Fujimori, D.
Citation:

Citation: Longbotham, J.; Kelly, M.; Fujimori, D.. "Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A"  ACS Chem. Biol. 18, 1915-1925 (2023).
PubMed: 33621062

Assembly members:

Assembly members:
entity_1, polymer, 59 residues, 6605.556 Da.
entity_2, polymer, 10 residues, 1150.332 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSVNFVDLYVCMFCGRGNNE DKLLLCDGCDDSYHTFCLIP PLPDVPKGDWRCPKCVAEE
entity_2: ARTKQTARKS

Data sets:
Data typeCount
13C chemical shifts201
15N chemical shifts53
1H chemical shifts450

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33
4unit_43

Entities:

Entity 1, unit_1 59 residues - 6605.556 Da.

1   GLYSERVALASNPHEVALASPLEUTYRVAL
2   CYSMETPHECYSGLYARGGLYASNASNGLU
3   ASPLYSLEULEULEUCYSASPGLYCYSASP
4   ASPSERTYRHISTHRPHECYSLEUILEPRO
5   PROLEUPROASPVALPROLYSGLYASPTRP
6   ARGCYSPROLYSCYSVALALAGLUGLU

Entity 2, unit_2 10 residues - 1150.332 Da.

1   ALAARGTHRLYSGLNTHRALAARGLYSSER

Entity 3, unit_3 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: Histone lysine demethylase 5A, KDM5A, [U-13C; U-15N], 900 uM; Histone H3.1 4000 uM; HEPES 50 mM; sodium chloride 150 mM; beta-mercaptoethanol 5 mM; ZnCl2 0.1 mM

sample_2: Histone lysine demethylase 5A, KDM5A, [U-13C; U-15N], 550 uM; Histone H3.1 800 uM; HEPES 50 mM; sodium chloride 150 mM; beta-mercaptoethanol 5 mM; ZnCl2 0.1 mM

sample_3: Histone lysine demethylase 5A, KDM5A, [U-13C; U-15N], 1250 uM; Histone H3.1 400 uM; HEPES 50 mM; sodium chloride 150 mM; beta-mercaptoethanol 5 mM; ZnCl2 0.1 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
CBCACONHsample_2isotropicsample_conditions_1
CBCANHsample_2isotropicsample_conditions_1
3D (H)CCCONH-TOCSYsample_1isotropicsample_conditions_1
3D H(CC)(CO)NH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
2D intra-peptide TOCSYsample_3isotropicsample_conditions_1
3D filtered intermolecular NOESYsample_1isotropicsample_conditions_1
C HSQCsample_1isotropicsample_conditions_1
N HSQCsample_1isotropicsample_conditions_1
3D NOESYsample_1isotropicsample_conditions_1
2D intra-peptide NOESYsample_3isotropicsample_conditions_1

Software:

ARIA v2.3.2, Linge, O'Donoghue and Nilges - refinement, structure calculation

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

  • Bruker AVANCE 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks