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- PDB-7k7a: Transmembrane structure of TNFR1 -

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Basic information

Entry
Database: PDB / ID: 7k7a
TitleTransmembrane structure of TNFR1
ComponentsTumor necrosis factor receptor superfamily member 1ACD120
KeywordsAPOPTOSIS / TRANSMEMBRANE HELIX
Function / homology
Function and homology information


positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / TNF signaling / TNFR1-mediated ceramide production / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / positive regulation of execution phase of apoptosis / prostaglandin metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / receptor complex / defense response to bacterium / inflammatory response / membrane raft / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, 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 1A / Tumor necrosis factor receptor 1A, N-terminal / Tumor necrosis factor receptor 1A, 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 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhao, L. / Chou, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH) United States
CitationJournal: Front Cell Dev Biol / Year: 2020
Title: The Diversity and Similarity of Transmembrane Trimerization of TNF Receptors.
Authors: Zhao, L. / Fu, Q. / Pan, L. / Piai, A. / Chou, J.J.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.name
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 1A
B: Tumor necrosis factor receptor superfamily member 1A
C: Tumor necrosis factor receptor superfamily member 1A


Theoretical massNumber of molelcules
Total (without water)10,1133
Polymers10,1133
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1920 Å2
ΔGint-26 kcal/mol
Surface area8470 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 1A / CD120 / Tumor necrosis factor receptor 1 / TNF-R1 / Tumor necrosis factor receptor type I / TNFR-I / p55 / p60


Mass: 3371.109 Da / Num. of mol.: 3 / Mutation: C223A, M233A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF1A, TNFAR, TNFR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19438

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D HN(CA)CO
142isotropic23D 1H-15N NOESY
153isotropic33D 1H-15N NOESY
163isotropic23D 1H-13C NOESY FOR METHYLS
172isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
bicelle10.7 mM [U-100% 13C; U-100% 15N; U-80% 2H] Protein, 20 mM sodium phosphate, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2Otriple res_sample90% H2O/10% D2O
bicelle30.4 mM [U-100% 13C] Protein A, 20 mM sodium phosphate, 50 mM DMPC, 100 mM DHPC, 0.4 mM [U-100% 2H; U-100% 15N] Protein B, 90% H2O/10% D2OInter_sample90% H2O/10% D2O
bicelle20.7 mM [U-100% 13C; U-100% 15N] Protein, 20 mM sodium phosphate, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2OIntra_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMProtein[U-100% 13C; U-100% 15N; U-80% 2H]1
20 mMsodium phosphatenatural abundance1
50 mMDMPCnatural abundance1
100 mMDHPCnatural abundance1
0.4 mMProtein A[U-100% 13C]3
20 mMsodium phosphatenatural abundance3
50 mMDMPCnatural abundance3
100 mMDHPCnatural abundance3
0.4 mMProtein B[U-100% 2H; U-100% 15N]3
0.7 mMProtein[U-100% 13C; U-100% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMDMPCnatural abundance2
100 mMDHPCnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: triple res / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7502
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
XEASYBartelschemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
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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