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- PDB-8dpx: Preligand association structure of DR5 -

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Basic information

Entry
Database: PDB / ID: 8dpx
TitlePreligand association structure of DR5
ComponentsTumor necrosis factor receptor superfamily member 10B
KeywordsAPOPTOSIS / preligand association structure / autoinhibition state
Function / homology
Function and homology information


TRAIL receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell ...TRAIL receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to endoplasmic reticulum stress / Cell surface interactions at the vascular wall / cellular response to mechanical stimulus / signaling receptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / positive regulation of apoptotic process / apoptotic process / cell surface / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). ...Tumour necrosis factor receptor 10 / Tumor necrosis factor receptor 10, N-terminal / Tumour necrosis factor receptor 10A/B, death domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 10B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDu, G. / Zhao, L. / Chou, J.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI150709 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140887 United States
CitationJournal: Cell Res. / Year: 2023
Title: Autoinhibitory structure of preligand association state implicates a new strategy to attain effective DR5 receptor activation.
Authors: Du, G. / Zhao, L. / Zheng, Y. / Belfetmi, A. / Cai, T. / Xu, B. / Heyninck, K. / Van Den Heede, K. / Buyse, M.A. / Fontana, P. / Bowman, M. / Lin, L.L. / Wu, H. / Chou, J.J.
History
DepositionJul 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 10B
B: Tumor necrosis factor receptor superfamily member 10B
C: Tumor necrosis factor receptor superfamily member 10B


Theoretical massNumber of molelcules
Total (without water)36,6983
Polymers36,6983
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3010 Å2
ΔGint-12 kcal/mol
Surface area22770 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 10B / Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL receptor 2 / TRAIL-R2


Mass: 12232.644 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186
Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: O14763

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic112D 1H-15N TROSY-HSQC
121isotropic113D HNCA
131isotropic113D HN(CO)CA
141isotropic113D HN(CA)CO
151isotropic113D HNCO
161isotropic113D HN(CA)CB
181isotropic113D HN(COCA)CB
172isotropic123D 1H-15N NOESY-TROSY
192isotropic143D 1H-15N NOESY-TROSY
1103isotropic143D 1H-15N NOESY-TROSY
1114isotropic1413C-filtered 1H-15N NOESY-TROSY
1123isotropic142D 1H-13C HSQC
1135isotropic123D 1H-15N NOESY-TROSY
1145isotropic123D 1H-13C NOESY aliphatic
1156isotropic122D 1H-15N TROSY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle1400 uM [U-100% 15N, U-100% 13C, U-85% 2H] DR5 ectodomain, 4.4 mM DGS-NTA (Ni), 44 mM DMPC, 88 mM D7PC, 95% H2O/5% D2O(15N,13C, 2H)-labeled DR5-ECD anchored to DMPC-D7PC bicelle with q = 0.5 for triple resonance experiments(15N, 13C, 2H)_sample95% H2O/5% D2O
bicelle2500 uM [U-100% 15N; U-100% 2H] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O(15N,2H)-labeled DR5-ECD anchored to DMPC-D7PC bicelle with q = 0.5 for measuring HN-HN NOEs(15N,2H)_sample95% H2O/5% D2O
bicelle3250 uM [U-100% 15N; U-100% 2H] Isotopically mixed DR5 ectodomain, 250 uM [U-100% 13C] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2OIsotopically mixed DR5-ECD anchored to DMPC-D7PC bicelle with q = 0.5 for measuring intermolecular NOEs using regular 15N-edited NOESYmixed_NOE_sample195% H2O/5% D2O
bicelle4250 uM [U-100% 13C; U-100% 15N; U-95% 2H] Isotopically mixed DR5 ectodomain, 250 uM DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2OIsotopically mixed DR5-ECD anchored to DMPC-D7PC bicelle with q = 0.5 for measuring intermolecular NOEs using 13C-filtered 15N-edited NOESYmixed_NOE_sample295% H2O/5% D2O
bicelle5500 uM [U-100% 13C; U-100% 15N] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O(15N,13C)-labeled DR5-ECD anchored to DMPC-D7PC bicelle with q = 0.5 for measuring both intra- and inter- molecular NOEs(15N,13C)_sample95% H2O/5% D2O
bicelle6400 uM [U-100% 15N, U-85% 2H] DR5 ectodomain, 4.4 mM DGS-NTA (Ni), 44 mM DMPC, 88 mM D7PC, 95% H2O/5% D2O(15N,2H)-labeled DR5-ECD anchored to DMPC-D7PC bicelle with q = 0.5 for performing paramagnetic probe titration analysisPPT_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMDR5 ectodomain[U-100% 15N, U-100% 13C, U-85% 2H]1
4.4 mMDGS-NTA (Ni)natural abundance1
44 mMDMPCnatural abundance1
88 mMD7PCnatural abundance1
500 uMDR5 ectodomain[U-100% 15N; U-100% 2H]2
5.5 mMDGS-NTA (Ni)natural abundance2
55 mMDMPCnatural abundance2
110 mMD7PCnatural abundance2
250 uMIsotopically mixed DR5 ectodomain[U-100% 15N; U-100% 2H]3
250 uMDR5 ectodomain[U-100% 13C]3
5.5 mMDGS-NTA (Ni)natural abundance3
55 mMDMPCnatural abundance3
110 mMD7PCnatural abundance3
250 uMIsotopically mixed DR5 ectodomain[U-100% 13C; U-100% 15N; U-95% 2H]4
250 uMDR5 ectodomainnatural abundance4
5.5 mMDGS-NTA (Ni)natural abundance4
55 mMDMPCnatural abundance4
110 mMD7PCnatural abundance4
500 uMDR5 ectodomain[U-100% 13C; U-100% 15N]5
5.5 mMDGS-NTA (Ni)natural abundance5
55 mMDMPCnatural abundance5
110 mMD7PCnatural abundance5
400 uMDR5 ectodomain[U-100% 15N, U-85% 2H]6
4.4 mMDGS-NTA (Ni)natural abundance6
44 mMDMPCnatural abundance6
88 mMD7PCnatural abundance6
Sample conditionsDetails: Sample condition for structural characterization at 37C
Ionic strength: 50 mM / Ionic strength err: 5 / Label: high_temperature / pH: 7.2 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.005 / Temperature: 310 K / Temperature err: 1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001cryoprobe
Bruker AVANCE NEOBrukerAVANCE NEO7002cryoprobe
Bruker AVANCEBrukerAVANCE8003cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
CcpNmr AnalysisVersion 2Vranken et aldata analysis
TALOS+Shendata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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