[English] 日本語
Yorodumi
- PDB-2na6: Transmembrane domain of mouse Fas/CD95 death receptor -

+
Open data


ID or keywords:

Loading...

-
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


FasL/ CD95L signaling / dendrite regeneration / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / regulation of myeloid cell differentiation / negative regulation of B cell activation / regulation of B cell differentiation / B cell mediated immunity ...FasL/ CD95L signaling / dendrite regeneration / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / inflammatory cell apoptotic process / regulation of myeloid cell differentiation / negative regulation of B cell activation / regulation of B cell differentiation / B cell mediated immunity / negative regulation of Schwann cell migration / tumor necrosis factor receptor activity / CD95 death-inducing signaling complex / lymphocyte apoptotic process / negative regulation of Schwann cell proliferation / regulation of hematopoietic progenitor cell differentiation / negative thymic T cell selection / necroptotic signaling pathway / apical dendrite / death-inducing signaling complex / motor neuron apoptotic process / regulation of T cell differentiation / regulation of stress-activated MAPK cascade / cellular response to lithium ion / activation-induced cell death of T cells / hepatocyte apoptotic process / T cell homeostasis / positive regulation of release of cytochrome c from mitochondria / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / response to glucocorticoid / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / secretory granule / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to toxic substance / sarcolemma / circadian rhythm / positive regulation of neuron apoptotic process / regulation of cell population proliferation / gene expression / protease binding / neuron apoptotic process / regulation of apoptotic process / calmodulin binding / positive regulation of apoptotic process / apical plasma membrane / membrane raft / external side of plasma membrane / neuronal cell body / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular region / identical protein binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more