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- PDB-6nhw: Structure of the transmembrane domain of the Death Receptor 5 - D... -

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Basic information

Entry
Database: PDB / ID: 6nhw
TitleStructure of the transmembrane domain of the Death Receptor 5 - Dimer of Trimer
ComponentsTumor necrosis factor receptor superfamily member 10B
KeywordsIMMUNE SYSTEM / Death Receptor 5 / transmembrane helix oligomer / transmembrane helix mediated signaling / preligand autoinhibition
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
AuthorsChou, J.J. / Pan, L. / Fu, Q. / Zhao, L. / Chen, W. / Piai, A. / Fu, T. / Wu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116898 United States
CitationJournal: Cell / Year: 2019
Title: Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling.
Authors: Pan, L. / Fu, T.M. / Zhao, W. / Zhao, L. / Chen, W. / Qiu, C. / Liu, W. / Liu, Z. / Piai, A. / Fu, Q. / Chen, S. / Wu, H. / Chou, J.J.
History
DepositionDec 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
D: Tumor necrosis factor receptor superfamily member 10B
E: Tumor necrosis factor receptor superfamily member 10B
F: Tumor necrosis factor receptor superfamily member 10B


Theoretical massNumber of molelcules
Total (without water)22,3546
Polymers22,3546
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Using a special method named OG-label (Chen et al: The Unusual Transmembrane Partition of the Hexameric Channel of the Hepatitis C Virus. Structure, 26(4):627-634 ...Evidence: assay for oligomerization, Using a special method named OG-label (Chen et al: The Unusual Transmembrane Partition of the Hexameric Channel of the Hepatitis C Virus. Structure, 26(4):627-634 (2018).), Inter-Chain NOEs
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3570 Å2
ΔGint-51 kcal/mol
Surface area21040 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/peptide
Tumor necrosis factor receptor superfamily member 10B / Death receptor 5 / TNF-related apoptosis-inducing ligand receptor 2 / TRAIL-R2


Mass: 3725.699 Da / Num. of mol.: 6 / Fragment: residues 208-242
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: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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
111isotropic1TROSY-HSQC
121isotropic1TROSY-HNCA
131isotropic1TROSY-HN(CO)CA
141isotropic1TROSY-HN(CA)CO
151isotropic1TROSY-HNCO
161isotropic23D 15N NOE-TROSY-HSQC
172isotropic33D 15N NOE-TROSY-HSQC
182isotropic32D 1H-13C HSQC aliphatic
192isotropic33D 13C NOE-HSQC
1103isotropic32D 1H-13C HSQC
1113isotropic33D 15N NOE-TROSY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.8 mM [U-13C; U-15N; 85%-2H] Transmembrane Domain of Death Receptor 5, 50 mM DMPC, 100 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O(15N, 13C, 85% 2H) labeled, reconstituted in DMPC/DHPC bicelles with q = 0.5NCD_sample95% H2O/5% D2O
bicelle20.8 mM [U-13C; U-15N] Transmembrane Domain of Death Receptor 5, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O(15N, 13C) labeled, reconstituted in DMPC/DHPC bicelles with q = 0.5 with the DMPC and DHPC acyl chains deuteratedNC_sample95% H2O/5% D2O
bicelle30.4 mM [U-15N; U-2H; 15%-13C] Transmembrane Domain of Death Receptor 5, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2OIsotope mixed sample for inter-chain NOE experiment.mixed_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMTransmembrane Domain of Death Receptor 5[U-13C; U-15N; 85%-2H]1
50 mMDMPCnatural abundance1
100 mMDHPCnatural abundance1
20 mMsodium phosphatenatural abundance1
0.8 mMTransmembrane Domain of Death Receptor 5[U-13C; U-15N]2
50 mMDMPC[acyl chain U-2H]2
100 mMDHPC[acyl chain U-2H]2
20 mMsodium phosphatenatural abundance2
0.4 mMTransmembrane Domain of Death Receptor 5[U-15N; U-2H; 15%-13C]3
50 mMDMPC[acyl chain U-2H]3
100 mMDHPC[acyl chain U-2H]3
20 mMsodium phosphatenatural abundance3
Sample conditionsIonic strength: 50 mM / Ionic strength err: 20 / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001cryogenic probe
Bruker AVANCEBrukerAVANCE7502cryogenic probe
Bruker AVANCEBrukerAVANCE9003cryogenic probe

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH3.851Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMRCCPNchemical shift assignment
XEASYBartels et al.chemical shift assignment
X-PLOR NIH3.851Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
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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