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- PDB-5zgg: NMR structure of p75NTR transmembrane domain in complex with NSC49652 -

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Basic information

Entry
Database: PDB / ID: 5zgg
TitleNMR structure of p75NTR transmembrane domain in complex with NSC49652
ComponentsTumor necrosis factor receptor superfamily member 16
KeywordsMEMBRANE PROTEIN / transmembrane / complex
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 / negative regulation of hair follicle development / negative regulation of fibroblast growth factor receptor signaling pathway / p75NTR negatively regulates cell cycle via SC1 / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...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 / negative regulation of hair follicle development / negative regulation of fibroblast growth factor receptor signaling pathway / p75NTR negatively regulates cell cycle via SC1 / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / nerve development / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / nerve growth factor binding / NADE modulates death signalling / Regulated proteolysis of p75NTR / hair follicle morphogenesis / NRAGE signals death through JNK / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / Rho protein signal transduction / fibroblast growth factor receptor signaling pathway / coreceptor activity / 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 / central nervous system development / positive regulation of apoptotic signaling pathway / axon guidance / intracellular protein transport / circadian regulation of gene expression / neuromuscular junction / small GTPase binding / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / transmembrane signaling receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of fibroblast proliferation / cell-cell junction / presynapse / glucose homeostasis / signaling receptor activity / amyloid-beta binding / growth cone / fibroblast proliferation / perikaryon / neuron apoptotic process / dendritic spine / postsynaptic density / calmodulin binding / endosome / ubiquitin protein ligase binding / cell surface / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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
Chem-9F6 / Tumor necrosis factor receptor superfamily member 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsLin, Z. / Ibanez, C.
Funding support China, 1items
OrganizationGrant numberCountry
Tianjin17JCYBJC24200 China
CitationJournal: Cell Chem Biol / Year: 2018
Title: A Small Molecule Targeting the Transmembrane Domain of Death Receptor p75NTRInduces Melanoma Cell Death and Reduces Tumor Growth.
Authors: Goh, E.T.H. / Lin, Z. / Ahn, B.Y. / Lopes-Rodrigues, V. / Dang, N.H. / Salim, S. / Berger, B. / Dymock, B. / Senger, D.L. / Ibanez, C.F.
History
DepositionMar 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _pdbx_nmr_software.name

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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 superfamily member 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6563
Polymers7,4312
Non-polymers2251
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, SDS PAGE
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area920 Å2
ΔGint-11 kcal/mol
Surface area5880 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 3715.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGFR, TNFRSF16 / Production host: Escherichia coli (E. coli) / Strain (production host): SoluBL21 / References: UniProt: P08138
#2: Chemical ChemComp-9F6 / (2E)-1-(2-hydroxyphenyl)-3-(pyridin-3-yl)prop-2-en-1-one


Mass: 225.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11NO2 / Feature type: SUBJECT OF INVESTIGATION

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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 aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D (H)CCH-TOCSY
171isotropic12D TOCSY
181isotropic13D NOESY
191isotropic12D 1H-13C filtered NOESY

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Sample preparation

DetailsType: micelle
Contents: 0.8 mM [U-99% 13C; U-99% 15N] p75NTR TMD, 3.9 mM 4809F6, 100 mM [U-98% 2H] DPC, 5 % [U-99.9% 2H] DMSO, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMp75NTR TMD[U-99% 13C; U-99% 15N]1
3.9 mM4809F6natural abundance1
100 mMDPC[U-98% 2H]1
5 %DMSO[U-99.9% 2H]1
Sample conditionsIonic strength: 20 mM / Label: condtions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 313 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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