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- PDB-3j6j: 3.6 Angstrom resolution MAVS filament generated from helical reco... -

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Basic information

Entry
Database: PDB / ID: 3j6j
Title3.6 Angstrom resolution MAVS filament generated from helical reconstruction
ComponentsMitochondrial antiviral-signaling protein
KeywordsIMMUNE SYSTEM / CARD / MAVS / innate immunity / RIG-I / MDA5 / spontaneous filament formation / seeded filament formation
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 / positive regulation of response to cytokine stimulus / protein localization to mitochondrion / 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 / 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 type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of viral genome replication / cellular response to exogenous dsRNA / type I interferon-mediated signaling pathway / 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 / molecular condensate scaffold activity / positive regulation of interferon-beta production / activation of innate immune response / 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 interleukin-6 production / positive regulation of protein import into nucleus / 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 / Caspase recruitment domain / Caspase recruitment domain / Death Domain, Fas / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mitochondrial antiviral-signaling protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsWu, B. / Peisley, A. / Li, Z. / Egelman, E. / Walz, T. / Penczek, P. / Hur, S.
CitationJournal: Mol Cell / Year: 2014
Title: Molecular imprinting as a signal-activation mechanism of the viral RNA sensor RIG-I.
Authors: Bin Wu / Alys Peisley / David Tetrault / Zongli Li / Edward H Egelman / Katharine E Magor / Thomas Walz / Pawel A Penczek / Sun Hur /
Abstract: RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires ...RIG-I activates interferon signaling pathways by promoting filament formation of the adaptor molecule, MAVS. Assembly of the MAVS filament is mediated by its CARD domain (CARD(MAVS)), and requires its interaction with the tandem CARDs of RIG-I (2CARD(RIG-I)). However, the precise nature of the interaction between 2CARD(RIG-I) and CARD(MAVS), and how this interaction leads to CARD(MAVS) filament assembly, has been unclear. Here we report a 3.6 Å electron microscopy structure of the CARD(MAVS) filament and a 3.4 Å crystal structure of the 2CARD(RIG-I):CARD(MAVS) complex, representing 2CARD(RIG-I) "caught in the act" of nucleating the CARD(MAVS) filament. These structures, together with functional analyses, show that 2CARD(RIG-I) acts as a template for the CARD(MAVS) filament assembly, by forming a helical tetrameric structure and recruiting CARD(MAVS) along its helical trajectory. Our work thus reveals that signal activation by RIG-I occurs by imprinting its helical assembly architecture on MAVS, a previously uncharacterized mechanism of signal transmission.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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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
G: Mitochondrial antiviral-signaling protein
I: Mitochondrial antiviral-signaling protein
L: Mitochondrial antiviral-signaling protein


Theoretical massNumber of molelcules
Total (without water)90,4158
Polymers90,4158
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 1 / Rise per n subunits: 5.13 Å / Rotation per n subunits: -101.1 °)

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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: 11301.820 Da / Num. of mol.: 8 / Fragment: N-terminal CARD domain (UNP residues 1-97) / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPS1, KIAA1271, MAVS, VISA / Plasmid: pET47b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q7Z434

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: MAVS filament / Type: COMPLEX / Details: infinite filament
Molecular weightValue: 0.15 MDa / Experimental value: YES
Buffer solutionName: 20 mM Tris, 150 mM NaCl / pH: 7.5 / Details: 20 mM Tris, 150 mM NaCl
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged Quantifoil R1.2/1.3 holey carbon grids
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: NITROGEN / Details: Plunged in liquid nitrogen (FEI VITROBOT MARK I)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Aug 10, 2013
Details: Movies were recorded at liquid nitrogen temperature with a K2 Summit direct detector device camera operated in super-resolution mode with dose-fractionation.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Calibrated magnification: 40410 X / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 31 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
EM imaging opticsEnergyfilter name: FEI
Image scansNum. digital images: 1863
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1PHENIXmodel fitting
2Helicon3D reconstruction
Helical symmertyAngular rotation/subunit: 101.1 ° / Axial rise/subunit: 5.13 Å / Axial symmetry: C1
3D reconstructionResolution: 3.64 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 1.1 Å / Actual pixel size: 1.1 Å
Details: The electron density map of the filament was reconstructed using a helical geometrically constrained reconstruction approach (Helicon).
Symmetry type: HELICAL
Atomic model buildingB value: 136.08 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient
Details: METHOD--local refinement REFINEMENT PROTOCOL--rigid body with TLS
RefinementResolution: 3.64→99.2 Å / SU ML: 0.87 / σ(F): 1 / Phase error: 37.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 1729 5.1 %
Rwork0.2377 32187 -
obs0.2397 33916 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 329.95 Å2 / Biso mean: 160.475 Å2 / Biso min: 88.63 Å2
Refinement stepCycle: LAST / Resolution: 3.64→99.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 0 0 6344
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076496
ELECTRON MICROSCOPYf_angle_d1.2578840
ELECTRON MICROSCOPYf_chiral_restr0.051968
ELECTRON MICROSCOPYf_plane_restr0.0051144
ELECTRON MICROSCOPYf_dihedral_angle_d14.6682352
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.64-3.74750.49341610.481327392900100
3.7475-3.86850.54061350.443325802715100
3.8685-4.00670.45691480.38727612909100
4.0067-4.16710.38051380.343826582796100
4.1671-4.35680.36181480.301827152863100
4.3568-4.58650.27721210.256726402761100
4.5865-4.87380.28981390.247627332872100
4.8738-5.25010.30921650.228726622827100
5.2501-5.77840.28211530.232126852838100
5.7784-6.61440.2621350.212127052840100
6.6144-8.33280.20911540.170226222776100
8.3328-99.23680.18071320.1752687281999
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON MICROSCOPY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.15543.68361.10942.52722.67186.91830.31520.22710.78262.323-0.9990.99661.75610.64280.00991.2080.1340.09161.21610.09931.070217.918717.288122.468
24.53431.23461.42525.47881.19433.82780.9578-0.163-0.04470.4086-0.66770.92820.07110.123-0.48921.1824-0.07240.04351.1219-0.05821.21169.9795.375511.6554
39.04071.97788.28982.11433.49498.99622.28271.6904-1.49831.3876-0.99522.25880.2202-0.4196-0.57821.05120.26180.1281.81420.02681.38128.83188.164417.2166
47.11060.82461.1879.30870.413510.126-1.1899-1.08711.4894-1.67060.0681-0.6925-0.0141-0.76720.6121.20620.1459-0.15251.1063-0.21231.254920.712415.846112.2792
51.81932.73211.8259.31982.2157.71914.2593-1.15046.15621.40390.21442.27785.38321.007-1.64582.9826-0.0814-0.89551.16390.1683-0.223725.8529-2.311841.1618
66.91122.98461.11072.11796.21516.5965-0.75261.45852.284-7.0671-0.36950.5416-2.8715-0.69461.38581.8846-0.1992-0.33541.17190.01811.962816.385-0.512428.3792
72.176-7.54931.54772.486-1.18157.4825-2.51840.28550.58170.85112.31520.0833-1.64242.38980.6111.5842-0.3114-0.06781.5664-0.25711.44727.649-9.568332.5115
82.36991.71772.93782.4222-0.93592.13321.333-1.72813.0902-2.3246-1.2423-2.43221.3565-0.10250.37441.1830.4568-0.03741.62220.24291.769212.878-2.391336.2322
98.49642.20614.13016.47631.73857.1297-0.12431.72731.00150.6287-0.62940.7619-1.63051.12110.62111.26760.0799-0.08451.24780.27981.385626.9496-5.420130.8811
101.8543-5.6991.77412.05190.38680.383-2.0424-1.7032.22161.71742.4558-0.50521.6314-3.0416-0.13041.8581-0.59730.1651.56170.24311.101913.7049-25.856527.0793
113.60670.06442.04828.0279-1.7254.1276-0.23021.24881.0695-0.32690.12240.0145-0.6171-0.6680.19611.0361-0.0611-0.30921.14970.08881.73593.5437-15.776616.6274
125.4123-5.02472.87997.1608-6.742210.0380.0254-0.40150.5937-1.36962.4870.7620.91781.1005-2.76721.8097-0.2844-0.12321.079-0.20341.77846.3784-15.141922.0899
139.3361-1.56220.45035.3220.17285.37930.39520.3151-1.5646-0.9929-0.8833-0.0702-0.62831.4516-0.00561.2814-0.04230.15691.06180.11891.198311.5766-28.337916.9017
148.78573.5551.76472.32543.74865.3352-0.92981.1223-0.07711.06361.19072.0415-1.11051.5309-0.33040.9585-0.0136-0.24831.50160.19841.4839-7.241425.050236.6432
155.05250.7732-0.44677.40933.89362.40360.46422.3307-0.1611-0.1761-0.38320.2713-0.0428-0.2729-0.04571.12060.20210.08891.5712-0.03361.1723-1.656711.794725.9685
162.101-0.05180.53526.97994.67922.250.72550.293-0.34621.04030.96080.40990.91810.2917-1.79021.3575-0.30690.01811.06650.01061.5682-4.719912.322431.6321
176.1128-0.899-2.76868.23152.42369.1520.65630.28420.0246-1.5637-2.13820.88181.1231-1.48951.17821.42250.0068-0.0081.2977-0.26181.1161-4.556526.556926.3529
182.2442-8.33644.17292.1223-3.93066.48951.2647-2.01590.6396-2.5641-1.2431-0.15191.7403-1.3667-0.30011.53050.03620.01161.05640.16451.448125.1897-8.46368.663
194.23064.21744.71032.41282.97692.731-0.1833-0.8570.6157-0.1226-0.12080.1771-0.1938-0.30970.59541.2928-0.0751-0.01761.0716-0.15781.292111.006-8.2897-2.4355
206.6831-6.37971.56532.0092-6.21199.41130.3394-0.68550.234-2.8538-0.63151.90051.20561.20730.561.77240.25870.29011.0366-0.13911.12212.5956-5.73513.282
2110.4125-0.67165.17085.14260.85789.046-0.86631.6647-0.43840.8907-1.2662-0.6102-1.4541.86041.63381.3021-0.1832-0.23441.20250.25461.660525.5416-11.5635-1.5996
222.09578.7358-0.60472.2928-1.68542.05840.45781.1402-1.19091.76960.2804-1.2892-0.848-1.7542-0.45711.03470.07250.15181.562-0.20641.1295-12.631-28.260813.0347
233.052-3.4621.02786.1477-3.37312.66840.59860.42460.14260.1742-0.51740.49570.3875-0.65690.17790.97090.02990.00461.1283-0.03551.4153-9.8326-14.12312.2858
242.09922.461-5.77945.3988-2.26668.22980.411.1611.73480.69360.4135-0.86660.8790.8445-0.46231.0053-0.2175-0.14481.7753-0.05061.1412-7.6878-16.36127.8493
255.22320.34691.05879.3348-4.84366.47250.0003-0.6791-0.4887-1.4208-0.7359-0.62141.14330.82220.49190.94870.09170.17941.44220.25591.4503-15.7459-28.00642.9821
261.9478-1.8-2.89072.25751.82850.9227-0.8734-2.5872-1.3989-2.0572-0.5290.2773-1.75790.06421.08211.6938-0.2427-0.26091.34270.16361.0423-24.515613.419617.7209
277.3831.7727-2.54873.22020.19573.083-1.09160.0436-1.0634-0.22781.01840.1957-0.8166-0.34420.41721.0584-0.0859-0.01990.99620.02581.5157-11.36887.82866.9247
289.5894-2.6197-1.63242.22028.04368.2263-0.576-1.5636-1.4572-1.81810.9664-0.72810.6162-0.8987-0.33291.6036-0.104-0.14080.96780.29321.2299-14.06396.12912.603
296.9521-1-1.42825.098-2.37456.87080.21021.67530.69290.1357-0.60290.51730.6007-0.3560.20931.2056-0.1650.06951.2725-0.19931.4033-23.649816.38587.7113
302.2901-6.8929-5.10166.81483.43673.69421.4646-0.0204-0.1645-0.2278-1.2522-0.442-1.9852-1.3406-0.06451.53850.40180.07560.9457-0.17411.4531-27.2918-13.2431.9258
314.50150.7352-1.9785.1847-3.43713.49190.28790.10370.1624-2.6988-0.6015-0.31350.10620.27910.38561.5099-0.01650.27050.9688-0.14151.4086-15.4763-5.085521.2677
321.9351-0.3068-2.69850.12881.03916.46410.2321-1.6823-2.3794-0.35510.54760.3451-1.02181.7576-0.94080.90970.06770.0041.3676-0.10481.709-15.3015-8.226727.0814
334.343-0.24420.71487.612-0.30488.4753-1.30980.6013-0.4380.7943-0.20621.50081.28371.2860.93741.09620.24210.12631.29810.05621.5897-29.2838-10.923521.6584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1chain 'A' and (resid 1 through 14 )A0
2ELECTRON MICROSCOPY2chain 'A' and (resid 15 through 49 )A0
3ELECTRON MICROSCOPY3chain 'A' and (resid 50 through 64 )A0
4ELECTRON MICROSCOPY4chain 'A' and (resid 65 through 97 )A0
5ELECTRON MICROSCOPY5chain 'B' and (resid 1 through 14 )B0
6ELECTRON MICROSCOPY6chain 'B' and (resid 15 through 30 )B0
7ELECTRON MICROSCOPY7chain 'B' and (resid 31 through 49 )B0
8ELECTRON MICROSCOPY8chain 'B' and (resid 50 through 64 )B0
9ELECTRON MICROSCOPY9chain 'B' and (resid 65 through 97 )B0
10ELECTRON MICROSCOPY10chain 'C' and (resid 1 through 14 )C0
11ELECTRON MICROSCOPY11chain 'C' and (resid 15 through 49 )C0
12ELECTRON MICROSCOPY12chain 'C' and (resid 50 through 64 )C0
13ELECTRON MICROSCOPY13chain 'C' and (resid 65 through 97 )C0
14ELECTRON MICROSCOPY14chain 'D' and (resid 1 through 14 )D0
15ELECTRON MICROSCOPY15chain 'D' and (resid 15 through 49 )D0
16ELECTRON MICROSCOPY16chain 'D' and (resid 50 through 64 )D0
17ELECTRON MICROSCOPY17chain 'D' and (resid 65 through 97 )D0
18ELECTRON MICROSCOPY18chain 'E' and (resid 1 through 14 )E0
19ELECTRON MICROSCOPY19chain 'E' and (resid 15 through 49 )E0
20ELECTRON MICROSCOPY20chain 'E' and (resid 50 through 64 )E0
21ELECTRON MICROSCOPY21chain 'E' and (resid 65 through 97 )E0
22ELECTRON MICROSCOPY22chain 'G' and (resid 1 through 14 )G0
23ELECTRON MICROSCOPY23chain 'G' and (resid 15 through 49 )G0
24ELECTRON MICROSCOPY24chain 'G' and (resid 50 through 64 )G0
25ELECTRON MICROSCOPY25chain 'G' and (resid 65 through 97 )G0
26ELECTRON MICROSCOPY26chain 'I' and (resid 1 through 14 )I0
27ELECTRON MICROSCOPY27chain 'I' and (resid 15 through 49 )I0
28ELECTRON MICROSCOPY28chain 'I' and (resid 50 through 64 )I0
29ELECTRON MICROSCOPY29chain 'I' and (resid 65 through 97 )I0
30ELECTRON MICROSCOPY30chain 'L' and (resid 1 through 14 )L0
31ELECTRON MICROSCOPY31chain 'L' and (resid 15 through 49 )L0
32ELECTRON MICROSCOPY32chain 'L' and (resid 50 through 64 )L0
33ELECTRON MICROSCOPY33chain 'L' and (resid 65 through 97 )L0

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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