BMRB Entry 30553

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30553
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
Structure of the transmembrane domain of the Death Receptor 5 - Dimer of Trimer
Deposition date:
2018-12-24
Original release date:
2019-02-22
Authors:
Chou, J.; Pan, L.; Fu, Q.; Zhao, L.; Chen, W.; Piai, A.; Fu, T.; Wu, H.
Citation:

Citation: Pan, Liqiang; Fu, Tian-Min; Zhao, Wenbin; Zhao, Linlin; Chen, Wen; Qiu, Chixiao; Liu, Wenhui; Liu, Zhijun; Piai, Alessandro; Fu, Qingshan; Chen, Shuqing; Wu, Hao; Chou, James. "Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling."  Cell 176, 1477-1489.e14 (2019).
PubMed: 30827683

Assembly members:

Assembly members:
entity_1, polymer, 36 residues, 3725.699 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)   Vector: pMM-LR6

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MPGSLSGIIIGVTVAAVVLI VAVFVCKSLLWKKVLP

Data sets:
Data typeCount
13C chemical shifts66
15N chemical shifts32
1H chemical shifts32

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_1, 31
4entity_1, 41
5entity_1, 51
6entity_1, 61

Entities:

Entity 1, entity_1, 1 36 residues - 3725.699 Da.

1   METPROGLYSERLEUSERGLYILEILEILE
2   GLYVALTHRVALALAALAVALVALLEUILE
3   VALALAVALPHEVALCYSLYSSERLEULEU
4   TRPLYSLYSVALLEUPRO

Samples:

sample_1: Transmembrane Domain of Death Receptor 5, [U-13C; U-15N; 85%-2H], 0.8 ± 0.1 mM; DMPC 50 ± 3 mM; DHPC 100 ± 3 mM; sodium phosphate 20 ± 2 mM

sample_2: Transmembrane Domain of Death Receptor 5, [U-13C; U-15N], 0.8 ± 0.1 mM; DMPC, [acyl chain U-2H], 50 ± 3 mM; DHPC, [acyl chain U-2H], 100 ± 3 mM; sodium phosphate 20 ± 2 mM

sample_3: Transmembrane Domain of Death Receptor 5, [U-15N; U-2H; 15%-13C], 0.4 ± 0.1 mM; DMPC, [acyl chain U-2H], 50 ± 3 mM; DHPC, [acyl chain U-2H], 100 ± 3 mM; sodium phosphate 20 ± 2 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
TROSY-HSQCsample_1isotropicsample_conditions_1
TROSY-HNCAsample_1isotropicsample_conditions_1
TROSY-HNCOCAsample_1isotropicsample_conditions_1
TROSY-HNCACOsample_1isotropicsample_conditions_1
TROSY-HNCOsample_1isotropicsample_conditions_1
3D 15N NOE-TROSY-HSQCsample_1isotropicsample_conditions_1
3D 15N NOE-TROSY-HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
3D 13C NOE-HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D 15N NOE-TROSY-HSQCsample_3isotropicsample_conditions_1

Software:

X-PLOR NIH v3.851, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

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

CcpNMR, CCPN - chemical shift assignment

XEASY, Bartels et al. - chemical shift assignment

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 750 MHz
  • Bruker Avance 900 MHz

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