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- PDB-2ms8: Solution NMR structure of MAVS CARD -

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Basic information

Entry
Database: PDB / ID: 2ms8
TitleSolution NMR structure of MAVS CARD
ComponentsMitochondrial antiviral-signaling protein
KeywordsPROTEIN BINDING / MAVS CARD
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / positive regulation of type I interferon-mediated signaling pathway ...positive regulation of IP-10 production / regulation of peroxisome organization / RIG-I binding / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of myeloid dendritic cell cytokine production / CARD domain binding / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / protein localization to mitochondrion / positive regulation of response to cytokine stimulus / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / positive regulation of type I interferon production / ubiquitin ligase complex / signaling adaptor activity / positive regulation of defense response to virus by host / activation of innate immune response / positive regulation of interferon-beta production / molecular condensate scaffold activity / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / positive regulation of tumor necrosis factor production / TRAF3-dependent IRF activation pathway / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / mitochondrial outer membrane / molecular adaptor activity / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / identical protein binding
Similarity search - Function
IPS1, CARD domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Caspase recruitment domain / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsSpehr, J. / He, L. / Luehrs, T. / Ritter, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure determination of helical filaments by solid-state NMR spectroscopy.
Authors: He, L. / Bardiaux, B. / Ahmed, M. / Spehr, J. / Konig, R. / Lunsdorf, H. / Rand, U. / Luhrs, T. / Ritter, C.
History
DepositionJul 25, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)11,8171
Polymers11,8171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitochondrial antiviral-signaling protein / MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein ...MAVS / CARD adapter inducing interferon beta / Cardif / Interferon beta promoter stimulator protein 1 / IPS-1 / Putative NF-kappa-B-activating protein 031N / Virus-induced-signaling adapter / VISA


Mass: 11817.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAVS, IPS1, KIAA1271, VISA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z434

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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 aromatic
1312D 1H-13C HSQC aliphatic
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CO)CA
1713D HN(CA)CB
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic
11213D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] MAVS CARD-1, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 300 uM / Component: MAVS CARD-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 50 / pH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
PROSAGuntertprocessing
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
UNIO_102.0.2Thorsten Herrmannstructure calculation
CNS1.2refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ATNOSHerrmann, Guntert and Wuthrichstructure solution
CANDID2Herrmann, Guntert and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1098
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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