[English] 日本語
Yorodumi
- PDB-6m6o: NMR SOLUTION STRUCTURE OF A C-FLIPs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m6o
TitleNMR SOLUTION STRUCTURE OF A C-FLIPs
ComponentsCASP8 and FADD-like apoptosis regulator
KeywordsAPOPTOSIS / c-FLIPS
Function / homology
Function and homology information


negative regulation of myoblast fusion / skeletal myofibril assembly / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 ...negative regulation of myoblast fusion / skeletal myofibril assembly / skeletal muscle atrophy / TRAIL signaling / CD95 death-inducing signaling complex / regulation of skeletal muscle satellite cell proliferation / ripoptosome / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / regulation of necroptotic process / positive regulation of extracellular matrix organization / skeletal muscle tissue regeneration / positive regulation of glomerular mesangial cell proliferation / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / negative regulation of hepatocyte apoptotic process / cysteine-type endopeptidase activity involved in execution phase of apoptosis / death receptor binding / positive regulation of hepatocyte proliferation / negative regulation of cellular response to transforming growth factor beta stimulus / execution phase of apoptosis / RIPK1-mediated regulated necrosis / negative regulation of cardiac muscle cell apoptotic process / response to testosterone / cellular response to nitric oxide / negative regulation of reactive oxygen species biosynthetic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / skeletal muscle tissue development / keratinocyte differentiation / enzyme activator activity / cellular response to epidermal growth factor stimulus / cellular response to dexamethasone stimulus / erythrocyte differentiation / cellular response to estradiol stimulus / negative regulation of extrinsic apoptotic signaling pathway / Regulation of TNFR1 signaling / wound healing / neuron differentiation / positive regulation of neuron projection development / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / positive regulation of canonical NF-kappaB signal transduction / protease binding / positive regulation of ERK1 and ERK2 cascade / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / proteolysis / cytoplasm / cytosol
Similarity search - Function
Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain ...Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
CASP8 and FADD-like apoptosis regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBai, Z.Q. / Hu, K.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Solution structure of c-FLIP death effector domains.
Authors: Bai, Z.Q. / Ma, X. / Liu, B. / Huang, T. / Hu, K.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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: CASP8 and FADD-like apoptosis regulator


Theoretical massNumber of molelcules
Total (without water)21,5881
Polymers21,5881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11550 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein CASP8 and FADD-like apoptosis regulator / Caspase homolog / CASH / Caspase-eight-related protein / Casper / Caspase-like apoptosis regulatory ...Caspase homolog / CASH / Caspase-eight-related protein / Casper / Caspase-like apoptosis regulatory protein / CLARP / Cellular FLICE-like inhibitory protein / c-FLIP / FADD-like antiapoptotic molecule 1 / FLAME-1 / Inhibitor of FLICE / I-FLICE / MACH-related inducer of toxicity / MRIT / Usurpin


Mass: 21588.219 Da / Num. of mol.: 1 / Mutation: F114G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFLAR, CASH, CASP8AP1, CLARP, MRIT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O15519

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic23D HNCA
141isotropic23D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic23D HNCO
171isotropic13D HBHA(CO)NH
181isotropic23D (H)CCH-COSY
191isotropic23D 1H-15N NOESY
1101isotropic23D 1H-13C NOESY

-
Sample preparation

DetailsType: solution
Contents: 0.6 nM [U-99% 13C; U-99% 15N] c-FLIPS, 1.0 nM EDTA-Na2, 1.0 nM TCEP, 0.02 % NaN3, 60 nM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O
Details: 0.6 mM. / Label: 13C,15N / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 nMc-FLIPS[U-99% 13C; U-99% 15N]1
1.0 nMEDTA-Na2natural abundance1
1.0 nMTCEPnatural abundance1
0.02 %NaN3natural abundance1
60 nMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 110 mM / Label: 1 / pH: 7.5 / Pressure: 1 Pa / Temperature: 298 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
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 10

+
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://pdbjlvh1.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