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- PDB-6jpd: Mouse receptor-interacting protein kinase 3 (RIP3) amyloid struct... -

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Basic information

Entry
Database: PDB / ID: 6jpd
TitleMouse receptor-interacting protein kinase 3 (RIP3) amyloid structure by solid-state NMR
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsPROTEIN FIBRIL / programmed necrosis / amyloid
Function / homology
Function and homology information


RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 ...RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / positive regulation of necroptotic process / regulation of reactive oxygen species metabolic process / non-canonical NF-kappaB signal transduction / activation of protein kinase activity / T cell homeostasis / necroptotic process / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / thymus development / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / T cell differentiation in thymus / defense response to virus / regulation of apoptotic process / amyloid fibril formation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / apoptotic process / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...RHIM domain / RIP homotypic interaction motif / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLID-STATE NMR / simulated annealing
AuthorsWu, X.L. / Hu, H. / Zhang, J. / Dong, X.Q. / Wang, J. / Schwieters, C. / Wang, H.Y. / Lu, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentMinistry of Science and Technology (China) 2017YFA0504804 China
CitationJournal: Nat Commun / Year: 2021
Title: The amyloid structure of mouse RIPK3 (receptor interacting protein kinase 3) in cell necroptosis.
Authors: Wu, X.L. / Hu, H. / Dong, X.Q. / Zhang, J. / Wang, J. / Schwieters, C.D. / Liu, J. / Wu, G.X. / Li, B. / Lin, J.Y. / Wang, H.Y. / Lu, J.X.
History
DepositionMar 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 3
B: Receptor-interacting serine/threonine-protein kinase 3
C: Receptor-interacting serine/threonine-protein kinase 3
D: Receptor-interacting serine/threonine-protein kinase 3
E: Receptor-interacting serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)47,2725
Polymers47,2725
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Dark field beam-tilt transmission electron microscopy.Obtain the mass-per-unit length value., X-ray powder diffraction, confirm the fibril distance pattern.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6910 Å2
ΔGint-24 kcal/mol
Surface area6420 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein
Receptor-interacting serine/threonine-protein kinase 3 / RIP-like protein kinase 3 / Receptor-interacting protein 3 / mRIP3


Mass: 9454.359 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk3, Rip3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9QZL0, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D CC DARR
1211anisotropic32D CC DARR
131anisotropic12D NCaCX
1201anisotropic32D NCaCX
141anisotropic12D NCOCX
1221anisotropic32D NCOCX
151anisotropic13D NCACX
1231anisotropic33D NCACX
161anisotropic13D NCOCX
1241anisotropic33D NCOCX
1171anisotropic12D NC TEDOR
1152anisotropic12D CC DARR
1142anisotropic12D NCaCX
1132anisotropic12D NCOCX
1162anisotropic12D NC TEDOR
1123anisotropic12D CC DARR
1113anisotropic12D NCaCX
1103anisotropic12D NCOCX
1183anisotropic12D NC TEDOR
184anisotropic22D NC TEDOR
174anisotropic12D CC DARR
1194anisotropic22D ChhC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
gel solid11 mg/mL [U-99% 13C; U-99% 15N] mouse rip3 fibril, H2Omouse rip3 fibrils, [U-99% 13C; U-99% 15N]H2O
gel solid21 mg/mL 99% 2-13C Glycerol; U-99% 15N mouse rip3 fibril, H2Omouse rip3 fibrils, 99% 15N, 99% 2-13C GlycerolH2O
gel solid31 mg/mL 99% 1,3-13C Glycerol; 99% 15N mouse rip3 fibril, H2Omouse rip3 fibrils, 99% 15N, 99% 1,3-13C GlycerolH2O
gel solid41 mg/mL [U-50% 13C; natural abundance N][natural abundance C13, U-50% N15] mouse rip3 fibril, H2Omouse rip3 fibrils, [U-50% 13C; natural abundance N][natural abundance C13, U-50% N15]H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mLmouse rip3 fibril[U-99% 13C; U-99% 15N]1
1 mg/mLmouse rip3 fibril99% 2-13C Glycerol; U-99% 15N2
1 mg/mLmouse rip3 fibril99% 1,3-13C Glycerol; 99% 15N3
1 mg/mLmouse rip3 fibril[U-50% 13C; natural abundance N][natural abundance C13, U-50% N15]4
Sample conditionsIonic strength: 0 mM / Label: H2O / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE7001303K
Bruker AVANCEBrukerAVANCE7002268K
Agilent DD2AgilentDD27003303K

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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