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- PDB-2n80: p75NTR DD:RhoGDI -

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Basic information

Entry
Database: PDB / ID: 2n80
Titlep75NTR DD:RhoGDI
Components
  • Rho GDP-dissociation inhibitor 1
  • Tumor necrosis factor receptor superfamily member 16
KeywordsSIGNALING PROTEIN / RhoGDI / p75NTR / death domain
Function / homology
Function and homology information


NFG and proNGF binds to p75NTR / dorsal aorta development / Ceramide signalling / death receptor activity / detection of temperature stimulus / 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 / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...NFG and proNGF binds to p75NTR / dorsal aorta development / Ceramide signalling / death receptor activity / detection of temperature stimulus / 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 / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / p75NTR negatively regulates cell cycle via SC1 / neurotrophin binding / regulation of synaptic vesicle cycle / nerve development / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / 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 / RHOC GTPase cycle / odontogenesis of dentin-containing tooth / intracellular glucose homeostasis / semaphorin-plexin signaling pathway / RHOH GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / immunological synapse / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / fibroblast growth factor receptor signaling pathway / coreceptor activity / positive regulation of apoptotic signaling pathway / RAC1 GTPase cycle / p75NTR recruits signalling complexes / presynaptic modulation of chemical synaptic transmission / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / GTPase activator activity / negative regulation of cell migration / central nervous system development / axon guidance / intracellular protein transport / circadian regulation of gene expression / Schaffer collateral - CA1 synapse / neuromuscular junction / small GTPase binding / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of protein localization / positive regulation of fibroblast proliferation / cell-cell junction / transmembrane signaling receptor activity / glucose homeostasis / 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 / Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Death Domain, Fas / Death Domain, Fas ...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 / Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Death Domain, Fas / Death Domain, Fas / 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 / Coagulation Factor XIII; Chain A, domain 1 / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Distorted Sandwich / Immunoglobulin E-set / Orthogonal Bundle / Mainly Beta / Mainly Alpha
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 / molecular dynamics
Model detailslowest energy, model1
AuthorsLin, Z. / Ibanez, C.F.
CitationJournal: Elife / Year: 2015
Title: Structural basis of death domain signaling in the p75 neurotrophin receptor
Authors: Lin, Z. / Tann, J.Y. / Goh, E.T. / Kelly, C. / Lim, K.B. / Gao, J.F. / Ibanez, C.F.
History
DepositionSep 30, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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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: Rho GDP-dissociation inhibitor 1


Theoretical massNumber of molelcules
Total (without water)30,0572
Polymers30,0572
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
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: 10172.332 Da / Num. of mol.: 1 / Fragment: UNP residues 334-427
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 Rho GDP-dissociation inhibitor 1 / Rho GDI 1 / Rho-GDI alpha


Mass: 19884.559 Da / Num. of mol.: 1 / Fragment: UNP residues 31-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGDIA, GDIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52565

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCA
1513D HN(CO)CA
1613D (H)CCH-TOCSY
1713D 13C,15N-filtered NOESY
1814D 13C, 15N-edited NOESY
1922D 1H-15N HSQC
11022D 1H-13C HSQC aliphatic
11122D 1H-13C HSQC aromatic
11223D HNCA
11323D HN(CO)CA
11423D (H)CCH-TOCSY
11523D 13C,15N-filtered NOESY
11624D 13C, 15N-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] p75NTR DD-1, 1 mM [U-98% 2H] DTT-2, 10 mM [U-98% 2H] HEPES-3, 1 mM EDTA-4, 1 mM sodium azide-5, 2 mM RhoGDI-6, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-99% 13C; U-99% 15N] RhoGDI-7, 2 mM p75NTR DD-8, 1 mM [U-98% 2H] DTT-9, 10 mM [U-98% 2H] HEPES-10, 1 mM EDTA-11, 1 mM sodium azide-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMp75NTR DD-1[U-99% 13C; U-99% 15N]1
1 mMDTT-2[U-98% 2H]1
10 mMHEPES-3[U-98% 2H]1
1 mMEDTA-41
1 mMsodium azide-51
2 mMRhoGDI-61
0.5 mMRhoGDI-7[U-99% 13C; U-99% 15N]2
2 mMp75NTR DD-82
1 mMDTT-9[U-98% 2H]2
10 mMHEPES-10[U-98% 2H]2
1 mMEDTA-112
1 mMsodium azide-122
Sample conditionsIonic strength: 10 / pH: 6.9 / Pressure: ambient / 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
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANAGuntert, Braun and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular 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 / Representative conformer: 1

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