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- PDB-7csq: Solution structure of the complex between p75NTR-DD and TRADD-DD -

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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 / death receptor activity / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / positive regulation of odontogenesis of dentin-containing tooth / tumor necrosis factor receptor superfamily complex / negative regulation of hair follicle development / death domain binding / negative regulation of fibroblast growth factor receptor signaling pathway ...NFG and proNGF binds to p75NTR / death receptor activity / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / positive regulation of odontogenesis of dentin-containing tooth / tumor necrosis factor receptor superfamily complex / negative regulation of hair follicle development / death domain binding / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Defective RIPK1-mediated regulated necrosis / p75NTR negatively regulates cell cycle via SC1 / neurotrophin binding / positive regulation of hair follicle development / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNF signaling / nerve development / Caspase activation via Death Receptors in the presence of ligand / 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 / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of endothelial cell apoptotic process / canonical NF-kappaB signal transduction / fibroblast growth factor receptor signaling pathway / Rho protein signal transduction / coreceptor activity / tumor necrosis factor-mediated signaling pathway / extrinsic apoptotic signaling pathway / signaling adaptor activity / presynaptic modulation of chemical synaptic transmission / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / axon guidance / negative regulation of cell migration / central nervous system development / positive regulation of apoptotic signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / intracellular protein transport / Regulation of TNFR1 signaling / circadian regulation of gene expression / neuromuscular junction / small GTPase binding / positive regulation of miRNA transcription / Regulation of necroptotic cell death / positive regulation of protein localization to nucleus / cytoplasmic side of plasma membrane / kinase binding / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / transmembrane signaling receptor activity / glucose homeostasis / cell-cell junction / cellular response to tumor necrosis factor / presynapse / signaling receptor activity / amyloid-beta binding / growth cone / fibroblast proliferation / protein-macromolecule adaptor activity / neuron apoptotic process / dendritic spine / perikaryon / positive regulation of canonical NF-kappaB signal transduction / cytoskeleton / receptor complex / calmodulin binding / postsynaptic density / 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 / identical protein binding / nucleus / membrane / plasma membrane / cytosol
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. ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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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

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Experimental details

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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

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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 / Pressure: 1 atm / Temperature: 301 K

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NMR measurement

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

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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

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