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- EMDB-5494: Cryo-EM structure of short shafted adenovirus type 5 complexed wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-5494
TitleCryo-EM structure of short shafted adenovirus type 5 complexed with factor X
Map dataReconstruction of Ad5 with short fiber in complex with factor X
Sample
  • Sample: Complex of Ad5-short-fiber with factor X
  • Virus: Human adenovirus 5
Keywordsshort shafted adenovirus type 5 / factor X / cryo-EM structure determination
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 11.1 Å
AuthorsDoronin K / Flatt JW / Di Paolo NC / Khare R / Kalyuzhniy O / Acchione M / Sumida JP / Ohto U / Shimizu T / Akashi-Takamura S ...Doronin K / Flatt JW / Di Paolo NC / Khare R / Kalyuzhniy O / Acchione M / Sumida JP / Ohto U / Shimizu T / Akashi-Takamura S / Miyake K / MacDonald JW / Bammler TK / Beyer RP / Farin FM / Stewart PL / Shayakhmetov DM
CitationJournal: Science / Year: 2012
Title: Coagulation factor X activates innate immunity to human species C adenovirus.
Authors: Konstantin Doronin / Justin W Flatt / Nelson C Di Paolo / Reeti Khare / Oleksandr Kalyuzhniy / Mauro Acchione / John P Sumida / Umeharu Ohto / Toshiyuki Shimizu / Sachiko Akashi-Takamura / ...Authors: Konstantin Doronin / Justin W Flatt / Nelson C Di Paolo / Reeti Khare / Oleksandr Kalyuzhniy / Mauro Acchione / John P Sumida / Umeharu Ohto / Toshiyuki Shimizu / Sachiko Akashi-Takamura / Kensuke Miyake / James W MacDonald / Theo K Bammler / Richard P Beyer / Frederico M Farin / Phoebe L Stewart / Dmitry M Shayakhmetov /
Abstract: Although coagulation factors play a role in host defense for "living fossils" such as horseshoe crabs, the role of the coagulation system in immunity in higher organisms remains unclear. We modeled ...Although coagulation factors play a role in host defense for "living fossils" such as horseshoe crabs, the role of the coagulation system in immunity in higher organisms remains unclear. We modeled the interface of human species C adenovirus (HAdv) interaction with coagulation factor X (FX) and introduced a mutation that abrogated formation of the HAdv-FX complex. In vivo genome-wide transcriptional profiling revealed that FX-binding-ablated virus failed to activate a distinct network of nuclear factor κB-dependent early-response genes that are activated by HAdv-FX complex downstream of TLR4/MyD88/TRIF/TRAF6 signaling. Our study implicates host factor "decoration" of the virus as a mechanism to trigger an innate immune sensor that responds to a misplacement of coagulation FX from the blood into intracellular macrophage compartments upon virus entry into the cell.
History
DepositionSep 10, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseOct 24, 2012-
UpdateNov 21, 2012-
Current statusNov 21, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.995
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.995
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5494.jpg

Downloads & links

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Map

FileDownload / File: emd_5494.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Ad5 with short fiber in complex with factor X
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.25 Å/pix.
x 640 pix.
= 1440. Å		2.25 Å/pix.
x 640 pix.
= 1440. Å		2.25 Å/pix.
x 640 pix.
= 1440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.995 / Movie #1: 0.995
Minimum - Maximum0.82250977 - 1.2732873
Average (Standard dev.)0.98747128 (±0.0360664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 1440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.252.252.25
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z1440.0001440.0001440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean0.8231.2730.987

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Supplemental data

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Sample components

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Entire : Complex of Ad5-short-fiber with factor X

EntireName: Complex of Ad5-short-fiber with factor X
Components
  • Sample: Complex of Ad5-short-fiber with factor X
  • Virus: Human adenovirus 5

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Supramolecule #1000: Complex of Ad5-short-fiber with factor X

SupramoleculeName: Complex of Ad5-short-fiber with factor X / type: sample / ID: 1000
Oligomeric state: 240 factor X molecules bind to one Ad virion
Number unique components: 2
Molecular weightTheoretical: 164 MDa

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Name.synonym: Human adenovirus type 5 with short fiber / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: Human adenovirus type 5 with short fiber
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 150 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1170 Å / T number (triangulation number): 25

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.6 / Details: 50mM Tris, 150mM NaCl, 2mM CaCl2, 2mM MgCl2
GridDetails: Quantifoil R2/4 holey carbon grids, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 6 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 300,000 times magnification
Legacy - Electron beam tilt params: 0
DetailsLow dose
DateNov 12, 2010
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: OTHER / Digitization - Sampling interval: 15 µm / Number real images: 1101 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 400000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 310000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected with an in-house script and processed using Frealign
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Frealign / Number images used: 520

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