BMRB Entry 31034

Name: Preligand association structure of DR5
Published: 2023-02-09

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PDB ID: 8dpx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31034
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SEGLCPPGHHISEDGRDCIS CKYGQDYSTHWNDLLFCLRC TRCDSGEVELSPCTTTRNTV CQCEEGTFREEDSPEMCRKC RTGCPRGMVKVGDCTPWSDI ECVHKESGD

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	348
15N chemical shifts	97
1H chemical shifts	386

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1
3	unit_3	1

Entities:

Entity 1, unit_1 109 residues - 12232.644 Da.

1

SER

GLU

GLY

LEU

CYS

PRO

GLY

HIS

2

ILE

SER

GLU

ASP

GLY

ARG

ASP

CYS

ILE

SER

3

CYS

LYS

TYR

GLY

GLN

ASP

TYR

SER

THR

HIS

4

TRP

ASN

ASP

LEU

PHE

CYS

LEU

ARG

CYS

5

THR

ARG

CYS

ASP

SER

GLY

GLU

VAL

GLU

LEU

6

SER

PRO

CYS

THR

ARG

ASN

THR

VAL

7

CYS

GLN

CYS

GLU

GLY

THR

PHE

ARG

GLU

8

GLU

ASP

SER

PRO

GLU

MET

CYS

ARG

LYS

CYS

9

ARG

THR

GLY

CYS

PRO

ARG

GLY

MET

VAL

LYS

10

VAL

GLY

ASP

CYS

THR

PRO

TRP

SER

ASP

ILE

11

GLU

CYS

VAL

HIS

LYS

GLU

SER

GLY

ASP

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY-HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY-TROSY	sample_2	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY-TROSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY-TROSY	sample_3	isotropic	sample_conditions_1
13C-filtered 1H-15N NOESY-TROSY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY-TROSY	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_5	isotropic	sample_conditions_1
2D 1H-15N TROSY-HSQC	sample_6	isotropic	sample_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