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- PDB-2n83: p75NTR DD:RIP2 CARD -

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Basic information

Entry
Database: PDB / ID: 2n83
Titlep75NTR DD:RIP2 CARD
Components
  • Receptor-interacting serine/threonine-protein kinase 2
  • Tumor necrosis factor receptor superfamily member 16
KeywordsSIGNALING PROTEIN/TRANSFERASE / RIP2 CARD / p75NTR / death domain / SIGNALING PROTEIN-TRANSFERASE complex
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 / response to interleukin-18 / negative regulation of hair follicle development / toll-like receptor 2 signaling pathway / positive regulation of T-helper 1 cell differentiation ...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 / response to interleukin-18 / negative regulation of hair follicle development / toll-like receptor 2 signaling pathway / positive regulation of T-helper 1 cell differentiation / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / p75NTR negatively regulates cell cycle via SC1 / positive regulation of cytokine-mediated signaling pathway / positive regulation of T-helper 1 type immune response / positive regulation of xenophagy / immature T cell proliferation in thymus / caspase binding / xenophagy / LIM domain binding / nerve growth factor binding / positive regulation of protein K63-linked ubiquitination / nucleotide-binding oligomerization domain containing 1 signaling pathway / nerve development / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / CARD domain binding / positive regulation of immature T cell proliferation in thymus / NADE modulates death signalling / CD4-positive, alpha-beta T cell proliferation / JUN kinase kinase kinase activity / cellular response to peptidoglycan / response to interleukin-12 / Regulated proteolysis of p75NTR / positive regulation of CD4-positive, alpha-beta T cell proliferation / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of macrophage cytokine production / positive regulation of peptidyl-tyrosine phosphorylation / toll-like receptor 4 signaling pathway / hair follicle morphogenesis / NRAGE signals death through JNK / response to exogenous dsRNA / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / cellular response to lipoteichoic acid / positive regulation of interferon-alpha production / positive regulation of endothelial cell apoptotic process / fibroblast growth factor receptor signaling pathway / canonical NF-kappaB signal transduction / stress-activated MAPK cascade / coreceptor activity / positive regulation of chemokine production / Rho protein signal transduction / JNK cascade / extrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / signaling adaptor activity / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / presynaptic modulation of chemical synaptic transmission / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / positive regulation of interferon-beta production / response to interleukin-1 / NRIF signals cell death from the nucleus / axon guidance / lipopolysaccharide-mediated signaling pathway / negative regulation of cell migration / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / central nervous system development / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / positive regulation of apoptotic signaling pathway / activated TAK1 mediates p38 MAPK activation / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / neuromuscular junction / intracellular protein transport / circadian regulation of gene expression / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / protein homooligomerization / positive regulation of interleukin-6 production / small GTPase binding / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / positive regulation of type II interferon production / Interleukin-1 signaling / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / cytokine-mediated signaling pathway / positive regulation of tumor necrosis factor production / cell-cell junction / Ovarian tumor domain proteases / transmembrane signaling receptor activity / Downstream TCR signaling
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 / Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. ...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 / Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Death Domain, Fas / Death Domain, Fas / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 2 / Tumor necrosis factor receptor superfamily member 16
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
DepositionOct 2, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2May 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: Receptor-interacting serine/threonine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)22,6482
Polymers22,6482
Non-polymers00
Water00
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: 10530.701 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 Receptor-interacting serine/threonine-protein kinase 2 / CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ...CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ICE-kinase / RIP-like-interacting CLARP kinase / Receptor-interacting protein 2 / RIP-2 / Tyrosine-protein kinase RIPK2


Mass: 12116.883 Da / Num. of mol.: 1 / Fragment: UNP residues 435-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092 / Production host: Escherichia coli (E. coli)
References: UniProt: O43353, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase

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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 HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D 13C,15N-filtered NOESY
1813D 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, 10 mM [U-98% 2H] DTT-2, 1 mM RIP2 CARD-3, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-99% 13C; U-99% 15N] RIP2 CARD-4, 1 mM p75NTR DD-5, 10 mM [U-98% 2H] DTT-6, 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
10 mMDTT-2[U-98% 2H]1
1 mMRIP2 CARD-31
0.5 mMRIP2 CARD-4[U-99% 13C; U-99% 15N]2
1 mMp75NTR DD-52
10 mMDTT-6[U-98% 2H]2
Sample conditionsPressure: ambient 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
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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