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- PDB-9m6m: Atomic-Level Architecture and Assembly Mechanism of High-order St... -

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Basic information

Entry
Database: PDB / ID: 9m6m
TitleAtomic-Level Architecture and Assembly Mechanism of High-order Structures of RIPK1 Fibril Network Revealed by Integrated Structural Biology
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsPROTEIN FIBRIL / necroptosis / RIPK1 / RHIM / ssNMR / protein / fibril / high-order fibril structure
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 / TRIF-mediated programmed cell death / ripoptosome assembly / positive regulation of miRNA processing ...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 / TRIF-mediated programmed cell death / ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / TNFR1-induced NF-kappa-B signaling pathway / death domain binding / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / Ovarian tumor domain proteases / IKK complex recruitment mediated by RIP1 / peptidyl-serine autophosphorylation / ripoptosome / programmed necrotic cell death / positive regulation of macrophage differentiation / T cell apoptotic process / TRP channels / necroptotic signaling pathway / Ub-specific processing proteases / death-inducing signaling complex / positive regulation of necroptotic process / negative regulation of necroptotic process / 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 phosphorylation / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of execution phase of apoptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / positive regulation of JNK cascade / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / positive regulation of protein phosphorylation / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / positive regulation of neuron apoptotic process / protein autophosphorylation / amyloid fibril formation / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / receptor complex / positive regulation of MAPK cascade / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / 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. / Wu, X. / Lu, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171185 China
National Natural Science Foundation of China (NSFC)32501072 China
National Natural Science Foundation of China (NSFC)32401022 China
CitationJournal: To Be Published
Title: Atomic-Level Architecture and Assembly Mechanism of High-order Structures of RIPK1 Fibril Network Revealed by Integrated Structural Biology
Authors: Liu, J. / Wu, X. / Lu, J.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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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)14,0855
Polymers14,0855
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 192structures 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: 2817.094 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): RossetaDE3
References: UniProt: Q60855, non-specific serine/threonine protein kinase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
343isotropic22D CH
121isotropic23D CaNH
131isotropic23D coCAcoNH
181isotropic13D hNCaCx
161isotropic13D hCANCOCX
1172isotropic12D TEDOR
1164isotropic12D TEDOR
211isotropic12D DARR 50ms
2151isotropic12D DARR 200ms
2141isotropic12D DARR 500ms
1112isotropic12D [2]-13C-DARR 50ms
1182isotropic12D [2]-13C-DARR 200ms
1132isotropic12D [2]-13C-DARR 500ms
1101isotropic12D NCACX
191isotropic12D NCOCX

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
fiber14.0 mg/uL [U-100% 13C] glucose, 1.5 mg/L [U-100% 15N] ammonium chloride, 50mM acetic acid buffer PH 5.0Uniformly-labelled 20mg13C,15N-Uniformly-labelled-ripk150mM acetic acid buffer PH 5.0
fiber24.0 mg/L [2-13C] glycerol, 1.5 mg/L [U-100% 15N] ammonium chloride, 50mM acetic acid buffer PH 5.0Sparsely-labelled,2-13C,15N-Labelled mripk1 was expressed in M9 medium prepared in 50mM acrtic acid buffer, sapmle 20 mg2-13C,15N-Sparsely-labelled-ripk150mM acetic acid buffer PH 5.0
fiber44.0 mg/L [2-13C] glycerol, 1.5 mg/L [U-100% 15N] ammonium chloride, 50mM acetic acid buffer PH 5.0Sparsely-labelled,1,3-13C,15N-Labelled mripk1 was expressed in M9 medium prepared in 50mM acrtic acid buffer, sapmle 20 mg1,3-13C,15N-Sparsely-labelled-ripk150mM acetic acid buffer PH 5.0
fiber34.0 mg/L [2-13C] glucose, 1.5 mg/L [U-100% 15N] ammonium chloride, 99 % [2H] 99% D2O, 100% D2O2H,13C,15N-Labelled mripk1 was expressed in M9 medium prepared in 99% D2O, sapmle 1 mgD2O labelled-ripk1100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4.0 mg/uLglucose[U-100% 13C]1
1.5 mg/Lammonium chloride[U-100% 15N]1
4.0 mg/Lglycerol[2-13C]2
1.5 mg/Lammonium chloride[U-100% 15N]2
4.0 mg/Lglycerol[2-13C]4
1.5 mg/Lammonium chloride[U-100% 15N]4
4.0 mg/Lglucose[2-13C]3
1.5 mg/Lammonium chloride[U-100% 15N]3
99 %99% D2O[2H]3
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
11mg/ml protein elution solution was dialyzed for 4 days at room temperature, 50mM acrtic acid buffer(pH 5.0) was replaced twice every 24h.0 mMConditions-151 Pa263 K
21mg/ml protein elution solution was dialyzed for 4 days at room temperature, 50mM acrtic acid buffer(pH 5.0) was replaced twice every 24h.0 mMConditions-25.0 Not defined1 Pa293 K
32H,13C,15N-Labelled mripk1 was expressed in M9 medium prepared in 99%D2O.1mg/ml protein elution solution was dialyzed for 4 days at room temperature, H2O was replaced twice every 24h.0 mMConditions-35.0 Not defined1 Pa279 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
SparkyLee W, Tonelli M, Markley JL.data analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyLee W, Tonelli M, Markley JL.chemical shift assignment
SparkyLee W, Tonelli M, Markley JL.peak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 192 / Conformers submitted total number: 10

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