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- PDB-8ib0: The amyloid structure of mouse RIPK1 RHIM-containing domain by so... -

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Basic information

Entry
Database: PDB / ID: 8ib0
TitleThe amyloid structure of mouse RIPK1 RHIM-containing domain by solid-state NMR
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsPROTEIN FIBRIL / Necroptosis / RIPK1 / RHIM / SSNMR
Function / homology
Function and homology information


TNF signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNFR1-induced proapoptotic signaling / Caspase activation via Death Receptors in the presence of ligand / RIPK1-mediated regulated necrosis / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway ...TNF signaling / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TNFR1-induced proapoptotic signaling / Caspase activation via Death Receptors in the presence of ligand / RIPK1-mediated regulated necrosis / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / TRIF-mediated programmed cell death / ripoptosome assembly involved in necroptotic process / death domain binding / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Ovarian tumor domain proteases / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / ripoptosome / programmed necrotic cell death / positive regulation of macrophage differentiation / T cell apoptotic process / necroptotic signaling pathway / peptidyl-serine autophosphorylation / TRP channels / death-inducing signaling complex / Ub-specific processing proteases / positive regulation of necroptotic process / negative regulation of necroptotic process / JUN kinase kinase kinase activity / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of reactive oxygen species metabolic process / necroptotic process / positive regulation of execution phase of apoptosis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of phosphorylation / tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / positive regulation of neuron apoptotic process / cellular response to tumor necrosis factor / positive regulation of protein phosphorylation / protein autophosphorylation / amyloid fibril formation / positive regulation of canonical NF-kappaB signal transduction / receptor complex / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding
Similarity search - Function
: / RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / 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 ...: / RIP1, Death domain / RHIM domain / RIP homotypic interaction motif / 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
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLID-STATE NMR / simulated annealing
AuthorsLiu, J. / Xialian, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171185 China
CitationJournal: Nat Commun / Year: 2024
Title: The structure of mouse RIPK1 RHIM-containing domain as a homo-amyloid and in RIPK1/RIPK3 complex.
Authors: Liu, J. / Wu, X.L. / Zhang, J. / Li, B. / Wang, H.Y. / Wang, J. / Lu, J.X.
History
DepositionFeb 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.2Aug 21, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 28, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 1
B: Receptor-interacting serine/threonine-protein kinase 1
C: Receptor-interacting serine/threonine-protein kinase 1
D: Receptor-interacting serine/threonine-protein kinase 1
E: Receptor-interacting serine/threonine-protein kinase 1


Theoretical massNumber of molelcules
Total (without water)13,5105
Polymers13,5105
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, The inter-molecular correlation peaks indicate in-registry conformation. Transmission electron microscopy images showed fibril strands. X-ray diffraction of fibrils ...Evidence: NMR Distance Restraints, The inter-molecular correlation peaks indicate in-registry conformation. Transmission electron microscopy images showed fibril strands. X-ray diffraction of fibrils showed 4.6A and 9.6A diffraction rings, characteristic of amyloid assembly.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7980 Å2
ΔGint-22 kcal/mol
Surface area6330 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 196structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Receptor-interacting serine/threonine-protein kinase 1 / Cell death protein RIP / Receptor-interacting protein 1 / RIP-1


Mass: 2702.006 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Gene ID: 19766 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk1, Rinp, Rip / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3)
References: UniProt: Q60855, 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
111isotropic12D DARR 50ms mixing
151isotropic12D NCACX
141isotropic12D NCOCX
231isotropic22D NH
222isotropic22D CH
171isotropic12D zTEDOR 6.4ms mixing
261isotropic23D CONH
281isotropic23D CANH
291isotropic23D COcaNH
1103isotropic12D DARR 50ms mixing
1111isotropic12D DARR 500ms mixing
1123isotropic12D DARR 400ms mixing
1131isotropic12D CHHC
3144isotropic12D NHHC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
fiber11 mg/mL [U-100% 13C; U-100% 15N] mouse RIPK1, 100% H2OUniformly 13C,15N-labeled sapmle 20mgUniformly 13C,15N-labeled100% H2O
fiber21 mg/L [U-100% 13C; U-100% 15N; 2H] mouse RIPK1, 100% H2O2H, 13C, 15N-labelled mRIPK1 was expressed in M9 medium prepared in 99.8% D2O, sapmle 1mg2H, 13C, 15N-labeled100% H2O
fiber31 mg/L [2-13C-glucose, U-100% 15N] mouse RIPK1, 100% H2O[2-13C]-glycerol, 15N-labeled sapmle 20mg[2-13C]-glycerol, 15N-labeled100% H2O
fiber41 g/L [U-100% 13C; U-100% 15N] mouse RIPK1, 100% H2O1:1 mixture of 13C and 15N-labeled1:1 mixture of 13C and 15N-labeled100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mLmouse RIPK1[U-100% 13C; U-100% 15N]1
1 mg/Lmouse RIPK1[U-100% 13C; U-100% 15N; 2H]2
1 mg/Lmouse RIPK1[2-13C-glucose, U-100% 15N]3
1 g/Lmouse RIPK1[U-100% 13C; U-100% 15N]4
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
11 mg/mL protein elution solution was dialyzed for 4 days using 3.5-kDa dialysis membranes in Milli-Q water (pH 7.5) at room temperature, water was replaced twice every 24 h.0 mMconditions_17.51 atm303 K
21 mg/mL protein elution solution was dialyzed for 4 days using 3.5-kDa dialysis membranes in Milli-Q water (pH 7.5) at room temperature, water was replaced twice every 24 h.0 mMconditions_27.51 Pa279 K
31:1 mixing protein elution solution was dialyzed for 4 days using 3.5-kDa dialysis membranes in Milli-Q water (pH 7.5) at room temperature, water was replaced twice every 24 h.0 mMconditions_37.51 Pa271 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker 3.2 mm HCN E free probeBruker3.2 mm HCN E free probe7001
Bruker 0.7 mm HCN probeBruker0.7 mm HCN probe7002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 196 / Conformers submitted total number: 10

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