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- PDB-2na6: Transmembrane domain of mouse Fas/CD95 death receptor -

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Basic information

Entry
Database: PDB / ID: 2na6
TitleTransmembrane domain of mouse Fas/CD95 death receptor
ComponentsTumor necrosis factor receptor superfamily member 6
KeywordsAPOPTOSIS / transmembrane helix trimer / transmembrane domain / proline-based motif / Structural Genomics / PSI-Biology / Membrane Protein Structures by Solution NMR / MPSbyNMR
Function / homology
Function and homology information


negative regulation of Schwann cell migration / FasL/ CD95L signaling / inflammatory cell apoptotic process / dendrite regeneration / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of myeloid cell differentiation / regulation of lymphocyte differentiation / motor neuron apoptotic process ...negative regulation of Schwann cell migration / FasL/ CD95L signaling / inflammatory cell apoptotic process / dendrite regeneration / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of myeloid cell differentiation / regulation of lymphocyte differentiation / motor neuron apoptotic process / cellular response to hyperoxia / Fas signaling pathway / lymphocyte apoptotic process / negative regulation of Schwann cell proliferation / B cell mediated immunity / negative thymic T cell selection / tumor necrosis factor receptor activity / activation-induced cell death of T cells / CD95 death-inducing signaling complex / cellular response to lithium ion / negative regulation of B cell activation / necroptotic signaling pathway / hepatocyte apoptotic process / spleen development / death-inducing signaling complex / T cell homeostasis / apical dendrite / regulation of stress-activated MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of reactive oxygen species biosynthetic process / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway in absence of ligand / neuron apoptotic process / extrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / gene expression / secretory granule / response to glucocorticoid / apoptotic signaling pathway / cellular response to amino acid starvation / circadian rhythm / positive regulation of protein-containing complex assembly / sarcolemma / response to toxic substance / kinase binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / protease binding / protein phosphatase binding / regulation of apoptotic process / nuclear body / calmodulin binding / apical plasma membrane / positive regulation of apoptotic process / membrane raft / external side of plasma membrane / apoptotic process / neuronal cell body / negative regulation of apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / : / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / 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). ...Fas receptor / Fas receptor, death domain / Fas receptor, N-terminal / 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 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsFu, Q. / Chou, J.J. / Wu, H. / Fu, T. / Membrane Protein Structures by Solution NMR (MPSbyNMR)
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Basis and Functional Role of Intramembrane Trimerization of the Fas/CD95 Death Receptor.
Authors: Fu, Q. / Fu, T.M. / Cruz, A.C. / Sengupta, P. / Thomas, S.K. / Wang, S. / Siegel, R.M. / Wu, H. / Chou, J.J.
History
DepositionDec 21, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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 6
B: Tumor necrosis factor receptor superfamily member 6
C: Tumor necrosis factor receptor superfamily member 6


Theoretical massNumber of molelcules
Total (without water)10,7413
Polymers10,7413
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 75structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Tumor necrosis factor receptor superfamily member 6 / Apo-1 antigen / Apoptosis-mediating surface antigen FAS / FASLG receptor


Mass: 3580.494 Da / Num. of mol.: 3 / Fragment: Helical transmembrane residues 167-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fas, Apt1, Tnfrsf6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P25446

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N TROSY HSQC
1223D TROSY HNCA
1323D TROSY HN(CO)CA
1423D TROSY HN(CA)CO
1523D TROSY HNCO
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1833D 1H-15N NOESY
1932D 1H-13C HSQC aliphatic
11032D 1H-15N TROSY HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Mouse Fas Transmembrane Domain, 60 mM [U-100% 2H] acyl chains DMPC, 120 mM [U-100% 2H] acyl chains DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N; U-85% 2H] Mouse Fas Transmembrane Domain, 60 mM DMPC, 120 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-100% 15N; U-100% 2H] Mouse Fas Transmembrane Domain, 0.5 mM [U-15% 13C] Mouse Fas Transmembrane Domain, 60 mM [U-100% 2H] acyl chains DMPC, 120 mM [U-100% 2H] acyl chains DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMouse Fas Transmembrane Domain-1[U-100% 13C; U-100% 15N]1
60 mMDMPC-2[U-100% 2H] acyl chains1
120 mMDHPC-3[U-100% 2H] acyl chains1
20 mMsodium phosphate-41
1 mMMouse Fas Transmembrane Domain-5[U-100% 13C; U-100% 15N; U-85% 2H]2
60 mMDMPC-62
120 mMDHPC-72
20 mMsodium phosphate-82
0.5 mMMouse Fas Transmembrane Domain-9[U-100% 15N; U-100% 2H]3
0.5 mMMouse Fas Transmembrane Domain-10[U-15% 13C]3
60 mMDMPC-11[U-100% 2H] acyl chains3
120 mMDHPC-12[U-100% 2H] acyl chains3
20 mMsodium phosphate-133
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 75 / Conformers submitted total number: 15

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