[English] 日本語
Yorodumi
- PDB-7csq: Solution structure of the complex between p75NTR-DD and TRADD-DD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7csq
TitleSolution structure of the complex between p75NTR-DD and TRADD-DD
Components
  • Tumor necrosis factor receptor superfamily member 16
  • Tumor necrosis factor receptor type 1-associated DEATH domain protein
KeywordsAPOPTOSIS / p75 NTR / death domain / TRADD
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / death receptor activity / positive regulation of odontogenesis of dentin-containing tooth / tumor necrosis factor receptor superfamily complex / death domain binding / negative regulation of hair follicle development / negative regulation of fibroblast growth factor receptor signaling pathway ...NFG and proNGF binds to p75NTR / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / death receptor activity / positive regulation of odontogenesis of dentin-containing tooth / tumor necrosis factor receptor superfamily complex / death domain binding / negative regulation of hair follicle development / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / p75NTR negatively regulates cell cycle via SC1 / Defective RIPK1-mediated regulated necrosis / neurotrophin binding / positive regulation of hair follicle development / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / nerve development / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / nerve growth factor binding / NADE modulates death signalling / Regulated proteolysis of p75NTR / death-inducing signaling complex / transmembrane receptor protein tyrosine kinase adaptor activity / tumor necrosis factor receptor binding / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / hair follicle morphogenesis / NRAGE signals death through JNK / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / Rho protein signal transduction / extrinsic apoptotic signaling pathway via death domain receptors / canonical NF-kappaB signal transduction / fibroblast growth factor receptor signaling pathway / coreceptor activity / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / p75NTR recruits signalling complexes / presynaptic modulation of chemical synaptic transmission / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / negative regulation of cell migration / TNFR1-induced NF-kappa-B signaling pathway / central nervous system development / positive regulation of apoptotic signaling pathway / Regulation of TNFR1 signaling / axon guidance / intracellular protein transport / circadian regulation of gene expression / neuromuscular junction / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / small GTPase binding / kinase binding / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / activation of cysteine-type endopeptidase activity involved in apoptotic process / transmembrane signaling receptor activity / positive regulation of fibroblast proliferation / cell-cell junction / presynapse / glucose homeostasis / signaling receptor activity / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / growth cone / fibroblast proliferation / perikaryon / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / dendritic spine / postsynaptic density / molecular adaptor activity / cytoskeleton / receptor complex / calmodulin binding / endosome / positive regulation of cell migration / positive regulation of apoptotic process / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / cell surface / signal transduction / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region ...TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / Tumour necrosis factor receptor 16 / Tumor necrosis factor receptor 16, N-terminal / Tumor necrosis factor receptor member 16, transmembrane domain / Tumor necrosis factor receptor member 16 trans-membrane 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 16 / Tumor necrosis factor receptor type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLin, Z. / Zhang, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis of NF-kappa B signaling by the p75 neurotrophin receptor interaction with adaptor protein TRADD through their respective death domains.
Authors: Zhang, N. / Kisiswa, L. / Ramanujan, A. / Li, Z. / Sim, E.W. / Tian, X. / Yuan, W. / Ibanez, C.F. / Lin, Z.
History
DepositionAug 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2May 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 16
B: Tumor necrosis factor receptor type 1-associated DEATH domain protein


Theoretical massNumber of molelcules
Total (without water)23,4672
Polymers23,4672
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1220 Å2
ΔGint-1 kcal/mol
Surface area12910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Tumor necrosis factor receptor superfamily member 16 / Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR / Low-affinity nerve growth factor receptor ...Gp80-LNGFR / Low affinity neurotrophin receptor p75NTR / Low-affinity nerve growth factor receptor / NGF receptor / p75 ICD


Mass: 10530.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGFR, TNFRSF16 / Production host: Escherichia coli (E. coli) / References: UniProt: P08138
#2: Protein Tumor necrosis factor receptor type 1-associated DEATH domain protein / TNFR1-associated DEATH domain protein / TNFRSF1A-associated via death domain


Mass: 12936.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRADD / Production host: Escherichia coli (E. coli) / References: UniProt: Q15628

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aromatic
131isotropic12D 1H-13C HSQC aliphatic
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D (H)CCH-TOCSY
171isotropic14D 13C, 15N-edited NOESY
181isotropic13D 13C, 15N-filtered NOESY

-
Sample preparation

DetailsType: solution
Contents: 0.2 mM [U-99% 13C; U-99% 15N] p75 neurotrophin receptor death domain, 2 mM [U-99% 13C; U-99% 15N] tumor necrosis factor receptor1-associated death domain protein, 50% H2O/50% D2O
Label: sample_1 / Solvent system: 50% H2O/50% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMp75 neurotrophin receptor death domain[U-99% 13C; U-99% 15N]1
2 mMtumor necrosis factor receptor1-associated death domain protein[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength units: Not defined / Label: sample_conditions_1 / pH: 5.0 / Pressure: 1 atm / Temperature: 301 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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://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