BMRB Entry 31034

Title:
Preligand association structure of DR5
Deposition date:
2022-07-17
Original release date:
2023-02-09
Authors:
Du, G.; Zhao, L.; Chou, J.
Citation:

Citation: Du, Gang; Zhao, Linlin; Zheng, Yumei; Belfetmi, Anissa; Cai, Tiantian; Xu, Boying; Heyninck, Karen; Van Den Heede, Kim; Buyse, Marie-Ange; Fontana, Pietro; Bowman, Michael; Lin, Lih-Ling; Wu, Hao; Chou, James Jeiwen. "Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation"  Cell Res. 33, 131-146 (2023).
PubMed: 36604598

Assembly members:

Assembly members:
entity_1, polymer, 109 residues, 12232.644 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: Komagataella pastoris

Data sets:
Data typeCount
13C chemical shifts348
15N chemical shifts97
1H chemical shifts386

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21
3unit_31

Entities:

Entity 1, unit_1 109 residues - 12232.644 Da.

1   SERGLUGLYLEUCYSPROPROGLYHISHIS
2   ILESERGLUASPGLYARGASPCYSILESER
3   CYSLYSTYRGLYGLNASPTYRSERTHRHIS
4   TRPASNASPLEULEUPHECYSLEUARGCYS
5   THRARGCYSASPSERGLYGLUVALGLULEU
6   SERPROCYSTHRTHRTHRARGASNTHRVAL
7   CYSGLNCYSGLUGLUGLYTHRPHEARGGLU
8   GLUASPSERPROGLUMETCYSARGLYSCYS
9   ARGTHRGLYCYSPROARGGLYMETVALLYS
10   VALGLYASPCYSTHRPROTRPSERASPILE
11   GLUCYSVALHISLYSGLUSERGLYASP

Samples:

sample_1: DR5 ectodomain, [U-100% 15N, U-100% 13C, U-85% 2H], 400 uM; DGS-NTA (Ni) 4.4 mM; DMPC 44 mM; D7PC 88 mM

sample_2: DR5 ectodomain, [U-100% 15N; U-100% 2H], 500 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM

sample_3: DR5 ectodomain, [U-100% 13C], 250 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM; Isotopically mixed DR5 ectodomain, [U-100% 15N; U-100% 2H], 250 uM

sample_4: DR5 ectodomain 250 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM; Isotopically mixed DR5 ectodomain, [U-100% 13C; U-100% 15N; U-95% 2H], 250 uM

sample_5: DR5 ectodomain, [U-100% 13C; U-100% 15N], 500 uM; DGS-NTA (Ni) 5.5 mM; DMPC 55 mM; D7PC 110 mM

sample_6: DR5 ectodomain, [U-100% 15N, U-85% 2H], 400 uM; DGS-NTA (Ni) 4.4 mM; DMPC 44 mM; D7PC 88 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.2; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSY-HSQCsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D 1H-15N NOESY-TROSYsample_2isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
3D 1H-15N NOESY-TROSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESY-TROSYsample_3isotropicsample_conditions_1
13C-filtered 1H-15N NOESY-TROSYsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D 1H-15N NOESY-TROSYsample_5isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_5isotropicsample_conditions_1
2D 1H-15N TROSY-HSQCsample_6isotropicsample_conditions_1

Software:

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

XEASY, Bartels et al. - data analysis

CcpNmr Analysis vVersion 2, Vranken et al - data analysis

TALOS+, Shen - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE NEO 700 MHz
  • Bruker AVANCE 800 MHz

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