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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


dorsal aorta development / NFG and proNGF binds to p75NTR / death receptor activity / Ceramide signalling / toll-like receptor 2 signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / p75NTR negatively regulates cell cycle via SC1 / nucleotide-binding oligomerization domain containing 1 signaling pathway / caspase binding ...dorsal aorta development / NFG and proNGF binds to p75NTR / death receptor activity / Ceramide signalling / toll-like receptor 2 signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / neurotrophin binding / p75NTR negatively regulates cell cycle via SC1 / nucleotide-binding oligomerization domain containing 1 signaling pathway / caspase binding / LIM domain binding / positive regulation of protein K63-linked ubiquitination / nerve growth factor binding / cellular response to muramyl dipeptide / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / CARD domain binding / NADE modulates death signalling / Regulated proteolysis of p75NTR / JUN kinase kinase kinase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / NRAGE signals death through JNK / positive regulation of interferon-alpha production / Rho protein signal transduction / positive regulation of endothelial cell apoptotic process / neuron apoptotic process / extrinsic apoptotic signaling pathway / positive regulation of interleukin-12 production / canonical NF-kappaB signal transduction / coreceptor activity / presynaptic modulation of chemical synaptic transmission / signaling adaptor activity / positive regulation of interferon-beta production / intracellular glucose homeostasis / negative regulation of cell migration / positive regulation of protein ubiquitination / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / positive regulation of interleukin-1 beta production / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / non-specific protein-tyrosine kinase / circadian regulation of gene expression / neuromuscular junction / activated TAK1 mediates p38 MAPK activation / non-membrane spanning protein tyrosine kinase activity / positive regulation of protein localization to nucleus / intracellular protein transport / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / protein homooligomerization / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / T cell receptor signaling pathway / cellular response to amyloid-beta / small GTPase binding / Interleukin-1 signaling / cell-cell junction / glucose homeostasis / positive regulation of tumor necrosis factor production / Ovarian tumor domain proteases / transmembrane signaling receptor activity / Downstream TCR signaling / nervous system development / amyloid-beta binding / presynapse / growth cone / signaling receptor activity / vesicle / dendritic spine / adaptive immune response / cytoskeleton / perikaryon / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / calmodulin binding / non-specific serine/threonine protein kinase / defense response to bacterium / endosome / postsynaptic density / positive regulation of apoptotic process / inflammatory response / signaling receptor binding / innate immune response / protein serine kinase activity / ubiquitin protein ligase binding / protein serine/threonine kinase activity / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding
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 / Death Domain, Fas / Death Domain, Fas / TNFR/NGFR family cysteine-rich region 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 / Receptor-interacting serine/threonine-protein kinase 2 / RIP2, CARD domain / 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 / Death domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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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