BMRB Entry 36293

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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/BMR36293
MolProbity Validation Chart

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Title:
membrane-bound PD-L1-CD
Deposition date:
2019-11-07
Original release date:
2021-08-02
Authors:
Maorong, W.; Bin, W.; Bo, O.
Citation:

Citation: Wen, Maorong; Cao, Yunlei; Wu, Bin; Xiao, Taoran; Cao, Ruiyu; Wang, Qian; Liu, Xiwei; Xue, Hongjuan; Yu, Yang; Lin, Jialing; Xu, Chenqi; Xu, Jie; OuYang, Bo. "PD-L1 degradation is regulated by electrostatic membrane association of its cytoplasmic domain"  Nat. Commun. 12, 5106-5106 (2021).
PubMed: 34429434

Assembly members:

Assembly members:
Programmed cell death 1 ligand 1, polymer, 33 residues, 3797.370 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Programmed cell death 1 ligand 1: GPRLRKGRMMDVKKCGIQDT NSKKQSDTHLEET

Data sets:
Data typeCount
13C chemical shifts134
15N chemical shifts37
1H chemical shifts223

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 33 residues - 3797.370 Da.

1   GLYPROARGLEUARGLYSGLYARGMETMET
2   ASPVALLYSLYSCYSGLYILEGLNASPTHR
3   ASNSERLYSLYSGLNSERASPTHRHISLEU
4   GLUGLUTHR

Samples:

sample_1: PD-L1-CD, [U-13C; U-15N; U-2H], 0.5 mM; DHPC 85 mM; DMPG 60 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: PD-L1-CD, [U-13C; U-15N], 0.5 mM; DHPC, [U-2H], 85 mM; DMPG, [U-2H], 60 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: PD-L1-CD, [U-15N; U-2H], 0.5 mM; DHPC, [U-2H], 85 mM; POPG 60 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACOsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESY for lipid NOEsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

Sparky, Goddard - chemical shift assignment, peak picking

TopSpin v3.5.5, Bruker Biospin - collection

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

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Varian DD2 800 MHz

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