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- PDB-8x8t: NMR structure of p75NTR juxtamembrane domain in complex with RhoG... -

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Basic information

Entry
Database: PDB / ID: 8x8t
TitleNMR structure of p75NTR juxtamembrane domain in complex with RhoGDI N-terminal domain containing a phosphorylation-mimicking S34D mutation
Components
  • Rho GDP-dissociation inhibitor 1
  • Tumor necrosis factor receptor superfamily member 16
KeywordsSIGNALING PROTEIN / Inhibitor / Complex / Signaling
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / death receptor activity / Rho GDP-dissociation inhibitor 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 ...NFG and proNGF binds to p75NTR / detection of temperature stimulus / dorsal aorta development / Ceramide signalling / death receptor activity / Rho GDP-dissociation inhibitor 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 / regulation of synaptic vesicle cycle / nerve growth factor binding / NADE modulates death signalling / Regulated proteolysis of p75NTR / regulation of Rho protein signal transduction / hair follicle morphogenesis / NRAGE signals death through JNK / odontogenesis of dentin-containing tooth / RHOC GTPase cycle / intracellular glucose homeostasis / Rho protein signal transduction / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / RHOH GTPase cycle / immunological synapse / RHOG GTPase cycle / fibroblast growth factor receptor signaling pathway / RHOA GTPase cycle / RAC2 GTPase cycle / coreceptor activity / RAC1 GTPase cycle / presynaptic modulation of chemical synaptic transmission / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / GTPase activator activity / negative regulation of cell migration / axon guidance / central nervous system development / intracellular protein transport / positive regulation of apoptotic signaling pathway / circadian regulation of gene expression / neuromuscular junction / Schaffer collateral - CA1 synapse / : / positive regulation of miRNA transcription / small GTPase binding / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / positive regulation of fibroblast proliferation / transmembrane signaling receptor activity / cell-cell junction / glucose homeostasis / regulation of protein localization / presynapse / signaling receptor activity / amyloid-beta binding / growth cone / fibroblast proliferation / perikaryon / neuron apoptotic process / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / endosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / cell surface / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / 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 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region ...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 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / 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 / Immunoglobulin E-set
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 16 / Rho GDP-dissociation inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLin, Z. / Li, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Embo Rep. / Year: 2024
Title: RhoGDI phosphorylation by PKC promotes its interaction with death receptor p75 NTR to gate axon growth and neuron survival.
Authors: Ramanujan, A. / Li, Z. / Ma, Y. / Lin, Z. / Ibanez, C.F.
History
DepositionNov 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: Rho GDP-dissociation inhibitor 1
B: Tumor necrosis factor receptor superfamily member 16


Theoretical massNumber of molelcules
Total (without water)13,5372
Polymers13,5372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4210 Å2
ΔGint-15 kcal/mol
Surface area8420 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 Rho GDP-dissociation inhibitor 1


Mass: 6875.394 Da / Num. of mol.: 1 / Mutation: S34D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGDIA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52565
#2: Protein Tumor necrosis factor receptor superfamily member 16


Mass: 6661.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NGFR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08138

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-15N HSQC
121anisotropic12D 1H-13C HSQC
131anisotropic13D CBCA(CO)NH
141anisotropic13D HN(CA)CB
151anisotropic13D H(CCCO)NH
161anisotropic13D CC(CO)NH
171anisotropic13D (H)CCH-TOCSY
181anisotropic13D 13C,13C-NOESY
191anisotropic13D 15N,13C-NOESY
1101anisotropic13D 13C,15N-filtered NOESY
1112anisotropic12D 1H-15N HSQC
1122anisotropic13D (H)CCH-TOCSY
1132anisotropic13D CBCA(CO)NH
1142anisotropic13D HN(CA)CB
1152anisotropic13D H(CCCO)NH
1162anisotropic13D CC(CO)NH
1172anisotropic13D 13C,13C-NOESY
1182anisotropic13D 15N,13C-NOESY
1192anisotropic13D 13C,15N-filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.8 mM [U-13C; U-15N] RhoGDI-NTD, 2.4 mM NA p75NTR-JMD, 90% H2O/10% D2O13C,15N_RhoGDI-NTD90% H2O/10% D2O
solution20.8 mM [U-13C; U-15N] p75NTR-JMD, 2.4 mM NA RhoGDI-NTD, 90% H2O/10% D2O13C,15N_p75NTR-JMD90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMRhoGDI-NTD[U-13C; U-15N]1
2.4 mMp75NTR-JMDNA1
0.8 mMp75NTR-JMD[U-13C; U-15N]2
2.4 mMRhoGDI-NTDNA2
Sample conditionsDetails: 10mM PIPES pH 6.8 / Ionic strength: 10 mM / Label: Buffer_A / pH: 6.8 / Pressure: 1 Pa / Temperature: 293 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
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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