BMRB Entry 36483

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36483

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Title:
NMR strucutre of chimeric protein for model of PHD-Stella complex
Deposition date:
2022-04-04
Original release date:
2025-10-26
Authors:
Kobayashi, N.; Konuma, T.; Arita, K.
Citation:

Citation: Hata, Keiichi; Kobayashi, Naohiro; Sugimura, Keita; Qin, Weihua; Haxholli, Deis; Chiba, Yoshie; Yoshimi, Sae; Hayashi, Gosuke; Onoda, Hiroki; Ikegami, Takahisa; Mulholland, Christopher; Nishiyama, Atsuya; Nakanishi, Makoto; Leonhardt, Heinrich; Konuma, Tsuyoshi; Arita, Kyohei. "Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger."  Nucleic Acids Res. 50, 12527-12542 (2022).
PubMed: 36420895

Assembly members:

Assembly members:
Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3, polymer, 126 residues, 14581.885 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: house mouse   Taxonomy ID: 10090   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mus musculus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3: GPLGSGPSCRFCKDDENKPC RKCACHVCGGREAPEKQLLC DECDMAFHLYCLKPPLTSVP PEPEWYCPSCRTDSRREVQS AFPKRRVRTLLSVLKDPIAK MRRLVRIEQRQKRLEGNEFE RDSEPF

Data sets:
Data typeCount
13C chemical shifts510
15N chemical shifts123
1H chemical shifts728

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_ZN2

Entities:

Entity 1, entity_1 126 residues - 14581.885 Da.

1   GLYPROLEUGLYSERGLYPROSERCYSARG
2   PHECYSLYSASPASPGLUASNLYSPROCYS
3   ARGLYSCYSALACYSHISVALCYSGLYGLY
4   ARGGLUALAPROGLULYSGLNLEULEUCYS
5   ASPGLUCYSASPMETALAPHEHISLEUTYR
6   CYSLEULYSPROPROLEUTHRSERVALPRO
7   PROGLUPROGLUTRPTYRCYSPROSERCYS
8   ARGTHRASPSERARGARGGLUVALGLNSER
9   ALAPHEPROLYSARGARGVALARGTHRLEU
10   LEUSERVALLEULYSASPPROILEALALYS
11   METARGARGLEUVALARGILEGLUGLNARG
12   GLNLYSARGLEUGLUGLYASNGLUPHEGLU
13   ARGASPSERGLUPROPHE

Entity 2, entity_ZN - Zn - 65.409 Da.

1   ZNZNZN

Samples:

PHD_Stella: Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3, [U-13C; U-15N], mM; sodium chloride 50 mM; sodium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

PHD_Stella_D2O: Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3, [U-13C; U-15N], mM; sodium chloride 50 mM; sodium phosphate 10 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 293 K

sample_conditions_2: ionic strength: 50 mM; pH: 7.0 pD; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCPHD_Stellaisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticPHD_Stellaisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticPHD_Stella_D2Oisotropicsample_conditions_2
3D HNCOPHD_Stellaisotropicsample_conditions_1
3D HN(CO)CAPHD_Stellaisotropicsample_conditions_1
3D HNCACBPHD_Stellaisotropicsample_conditions_1
3D CBCA(CO)NHPHD_Stellaisotropicsample_conditions_1
2D 1H-13C HSQC aromaticPHD_Stellaisotropicsample_conditions_1
2D 1H-13C HSQC aromaticPHD_Stella_D2Oisotropicsample_conditions_2
3D HCCH-TOCSYPHD_Stellaisotropicsample_conditions_1
3D H(CCO)NHPHD_Stellaisotropicsample_conditions_1
3D C(CO)NHPHD_Stellaisotropicsample_conditions_1
3D 1H-15N NOESYPHD_Stellaisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticPHD_Stellaisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticPHD_Stella_D2Oisotropicsample_conditions_2
3D 1H-13C NOESY aromaticPHD_Stellaisotropicsample_conditions_1

Software:

TopSpin v3.5, Bruker Biospin - collection

NMRPipe v2017, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - chemical shift assignment

MAGRO v2.01.41, Kobayashi, N. - peak picking

NMRViewJ v9, Johnson, B. J. - data analysis

CYANA v3.98, Guntert, Mumenthaler and Wuthrich - structure calculation

Amber v12, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker AVANCE III 500 MHz
  • Bruker AVANCE III 800 MHz

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