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- EMDB-5890: Cryo-EM structure of MAVS CARD filament -

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Basic information

Entry
Database: EMDB / ID: 5890
TitleCryo-EM structure of MAVS CARD filament
KeywordsInnate immunity / helical filament
SampleMAVS CARD filament
SourceHomo sapiens / human
Map dataCryo-EM map of MAVS CARD filament
Methodhelical reconstruction, at 9.6 Å resolution
AuthorsXu H / He X / Zheng H / Huang LJ / Hou F / Yu Z / de la Cruz MJ / Borkowski B / Zhang X / Chen ZJ / Jiang Q-X
CitationElife, 2014, 3, e01489-e01489

Elife, 2014, 3, e01489-e01489 StrPapers
Structural basis for the prion-like MAVS filaments in antiviral innate immunity.
Hui Xu / Xiaojing He / Hui Zheng / Lily J Huang / Fajian Hou / Zhiheng Yu / Michael Jason de la Cruz / Brian Borkowski / Xuewu Zhang / Zhijian J Chen / Qiu-Xing Jiang

Validation ReportPDB-ID: 3j6c

SummaryFull reportAbout validation report
DateDeposition: Jan 22, 2014 / Header (metadata) release: Feb 19, 2014 / Map release: Mar 5, 2014 / Last update: Oct 7, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.52
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.52
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3j6c
  • Surface level: 0.52
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3j6c
  • Surface level: 0.52
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

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Map

Fileemd_5890.map.gz (map file in CCP4 format, 978 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.33 Å/pix.
= 233.3 Å
50 pix
2.33 Å/pix.
= 116.65 Å
50 pix
2.33 Å/pix.
= 116.65 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.333 Å
Density
Contour Level:0.52 (by author), 0.52 (movie #1):
Minimum - Maximum-4.69236183 - 6.60222197
Average (Standard dev.)0.36144659 (0.89477062)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions5050100
Origin000
Limit494999
Spacing5050100
CellA: 116.649994 Å / B: 116.649994 Å / C: 233.29999 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.3332.3332.333
M x/y/z5050100
origin x/y/z0.0000.0000.000
length x/y/z116.650116.650233.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS5050100
D min/max/mean-4.6926.6020.361

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Supplemental data

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Sample components

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Entire MAVS CARD filament

EntireName: MAVS CARD filament / Number of components: 1 / Oligomeric State: polymer
MassTheoretical: 546 kDa

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Component #1: protein, Mitochondrial antiviral-signaling protein (MAVS)

ProteinName: Mitochondrial antiviral-signaling protein (MAVS) / a.k.a: IPS1, KIAA1271, VISA / Oligomeric Details: polymer / Recombinant expression: Yes
MassTheoretical: 13 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Vector: pcDNA3 / Cell of expression system: HEK293T
External referencesUniProt: UniProt: Q7Z434

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C3 (3 fold cyclic) / Hand: LEFT HANDED / Delta z: 16.8 Å / Delta phi: 53.6 deg.
Sample solutionBuffer solution: 20mM Tris-HCl, 50mM NaCl, 1mM DTT / pH: 7.5
Support filmQuantifoil grids coated with thin carbon on top
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS / Date: Oct 20, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal), 61950 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 100,000x magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2000 nm / Energy filter: JEOL omega filter / Energy window: 0-35 eV
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns / URL of raw data: http://dx.doi.org/10.6019/EMPIAR-10014
Raw dataEMPIAR-10014 (Title: MAVS CARD and DeltaProTM filaments / Data size: 35.3 GB / Data #1: CARD set1 micrographs [micrographs - single frame] / Data #2: CARD set2 micrographs [micrographs - single frame] / Data #3: CARD set3 micrographs [micrographs - single frame] / Data #4: CARD set4 micrographs [micrographs - single frame]
Data #5: CARD set1 segments [picked particles - single frame - unprocessed]
Data #6: CARD set2 segments [picked particles - single frame - unprocessed]
Data #7: CARD set3 segments [picked particles - single frame - unprocessed]
Data #8: CARD set4 segments [picked particles - single frame - unprocessed]
Data #9: DeltProTM micrographs [micrographs - single frame]
Data #10: DeltaProTM segments [picked particles - single frame - unprocessed])

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Image processing

ProcessingMethod: helical reconstruction / Details: IHRSR
3D reconstructionAlgorithm: IHRSR / Software: Spider, MRC, EMAN, IMAGIC4D / CTF correction: Each filament segment
Details: Final data were calculated from three separate datasets from three sessions of data collection. The handedness of the map was determined by cryo-electron tomography.
Resolution: 9.6 Å / Resolution method: FSC 0.5, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera, SITUS / Refinement protocol: rigid body / Refinement space: REAL
Details: The docking of one X-ray model into a segmented map corresponding to one subunit was first done manually in Chimera, and then optimized using SITUS.
Input PDB model: 2VGQ
Chain ID: A
Output model

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