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- PDB-2ms7: High-resolution solid-state NMR structure of the helical signal t... -

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Basic information

Entry
Database: PDB / ID: 2ms7
TitleHigh-resolution solid-state NMR structure of the helical signal transduction filament MAVS CARD
ComponentsMitochondrial antiviral-signaling protein
KeywordsPROTEIN BINDING / MAVS CARD filament
Function / homology
Function and homology information


positive regulation of IP-10 production / regulation of peroxisome organization / 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 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane ...positive regulation of IP-10 production / regulation of peroxisome organization / 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 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / positive regulation of type I interferon-mediated signaling pathway / peroxisomal membrane / TRAF6 mediated IRF7 activation / negative regulation of viral genome replication / cytoplasmic pattern recognition receptor signaling pathway / type I interferon-mediated signaling pathway / cellular response to exogenous dsRNA / positive regulation of NLRP3 inflammasome complex assembly / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / positive regulation of type I interferon production / ubiquitin ligase complex / positive regulation of defense response to virus by host / signaling adaptor activity / antiviral innate immune response / activation of innate immune response / protein serine/threonine kinase binding / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / Negative regulators of DDX58/IFIH1 signaling / molecular condensate scaffold activity / mitochondrial membrane / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Evasion by RSV of host interferon responses / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of tumor necrosis factor production / SARS-CoV-1 activates/modulates innate immune responses / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / protein-macromolecule adaptor activity / molecular adaptor activity / defense response to virus / DNA-binding transcription factor binding / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / defense response to bacterium / 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)
MethodSOLID-STATE NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHe, L. / Bardiaux, B. / Spehr, J. / 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 1.2May 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial antiviral-signaling protein
B: Mitochondrial antiviral-signaling protein
C: Mitochondrial antiviral-signaling protein
D: Mitochondrial antiviral-signaling protein
E: Mitochondrial antiviral-signaling protein
F: Mitochondrial antiviral-signaling protein
G: Mitochondrial antiviral-signaling protein
H: Mitochondrial antiviral-signaling protein
I: Mitochondrial antiviral-signaling protein
J: Mitochondrial antiviral-signaling protein
K: Mitochondrial antiviral-signaling protein
L: Mitochondrial antiviral-signaling protein
M: Mitochondrial antiviral-signaling protein
N: Mitochondrial antiviral-signaling protein
O: Mitochondrial antiviral-signaling protein
P: Mitochondrial antiviral-signaling protein
Q: Mitochondrial antiviral-signaling protein
R: Mitochondrial antiviral-signaling protein
S: Mitochondrial antiviral-signaling protein
T: Mitochondrial antiviral-signaling protein
U: Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)248,16521
Polymers248,16521
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)15 / 500structures with the lowest energy
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.: 21 / Fragment: UNP RESIDUES 1-100
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: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DARR
1213D NCACX
1313D NCOCX
1413D CANCO
1512D PDSD
1612D PAIN
1712D NCA
1862D NCX

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM [U-99% 13C; U-99% 15N] MAVS CARD-1, H2OH2O
220 mM [1-13C]-Glc U-15N MAVS CARD-2, H2OH2O
320 mM [2-13C]-Glc U-15N MAVS CARD-3, H2OH2O
420 mM [1/2-13C]-Glc(mixed) U15N MAVS CARD-4, H2OH2O
520 mM [U-99% 13C; U-99% 15N] 1:6(Unlabeled) Diluted sample MAVS CARD-5, H2OH2O
620 mM U15N mixed with U13C labeled sample MAVS CARD-6, H2OH2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMAVS CARD-1[U-99% 13C; U-99% 15N]1
20 mMMAVS CARD-2[1-13C]-Glc U-15N2
20 mMMAVS CARD-3[2-13C]-Glc U-15N3
20 mMMAVS CARD-4[1/2-13C]-Glc(mixed) U15N4
20 mMMAVS CARD-5[U-99% 13C; U-99% 15N] 1:6(Unlabeled) Diluted sample5
20 mMMAVS CARD-6U15N mixed with U13C labeled sample6
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 278 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
CcpNmrCCPNdata analysis
CcpNmrCCPNchemical shift assignment
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.3.2Linge, O'Donoghue and Nilgesdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
TALOSCornilescu, Delaglio and Baxdata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
ARIA/CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Simulated annealing with helical symmetry constrained by strict NCS.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 15 / Representative conformer: 1

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