+Open data
-Basic information
Entry | Database: PDB / ID: 2n80 | ||||||
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Title | p75NTR DD:RhoGDI | ||||||
Components |
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Keywords | SIGNALING PROTEIN / RhoGDI / p75NTR / death domain | ||||||
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 / 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 / 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 / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / CDC42 GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / Rho protein signal transduction / immunological synapse / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / fibroblast growth factor receptor signaling pathway / coreceptor activity / 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 / negative regulation of cell migration / GTPase activator activity / central nervous system development / positive regulation of apoptotic signaling pathway / 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 / transmembrane signaling receptor activity / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of protein localization / 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 / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Lin, Z. / Ibanez, C.F. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2n80.cif.gz | 813.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2n80.ent.gz | 688.6 KB | Display | PDB format |
PDBx/mmJSON format | 2n80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2n80_validation.pdf.gz | 431.4 KB | Display | wwPDB validaton report |
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Full document | 2n80_full_validation.pdf.gz | 542.5 KB | Display | |
Data in XML | 2n80_validation.xml.gz | 51.5 KB | Display | |
Data in CIF | 2n80_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/2n80 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/2n80 | HTTPS FTP |
-Related structure data
Related structure data | 2n7zC 2n83C 2n97C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 10 / pH: 6.9 / Pressure: ambient / Temperature: 301 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1 |