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

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Database: EMDB / ID: 5494
TitleCryo-EM structure of short shafted adenovirus type 5 complexed with factor X
Keywordsshort shafted adenovirus type 5 / factor X / cryo-EM structure determination
SampleComplex of Ad5-short-fiber with factor X
SourceHuman adenovirus 5 / virus / Human adenovirus type 5 with short fiber
Map dataReconstruction of Ad5 with short fiber in complex with factor X
Methodsingle particle (icosahedral) reconstruction, at 11.1 Å resolution
AuthorsDoronin 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
CitationScience, 2012, 338, 795-798

Science, 2012, 338, 795-798 Yorodumi Papers
Coagulation factor X activates innate immunity to human species C adenovirus.
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

DateDeposition: Sep 10, 2012 / Header (metadata) release: Sep 26, 2012 / Map release: Oct 24, 2012 / Last update: Nov 21, 2012

Structure visualization

  • 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
3D viewer
Supplemental images

Downloads & links


Fileemd_5494.map.gz (map file in CCP4 format, 1024001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
640 pix
2.25 Å/pix.
= 1440. Å
640 pix
2.25 Å/pix.
= 1440. Å
640 pix
2.25 Å/pix.
= 1440. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.25 Å
Contour Level:0.995 (by author), 0.995 (movie #1):
Minimum - Maximum0.82250977 - 1.2732873
Average (Standard dev.)0.98747128 (0.0360664)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1440 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ-5029166
MAP C/R/S123
start NC/NR/NS-320-320-320
D min/max/mean0.8231.2730.987

Supplemental data

Sample components

Entire Complex of Ad5-short-fiber with factor X

EntireName: Complex of Ad5-short-fiber with factor X / Number of components: 2
Oligomeric State: 240 factor X molecules bind to one Ad virion
MassTheoretical: 164 MDa

Component #1: virus, Human adenovirus 5

VirusName: Human adenovirus 5 / a.k.a: Human adenovirus type 5 with short fiber / Class: VIRION / Empty: No / Enveloped: No / Isolate: OTHER
MassTheoretical: 150 MDa
SpeciesSpecies: Human adenovirus 5 / virus / Human adenovirus type 5 with short fiber
Source (natural)Host Species: Homo sapiens / human / Wikipedia / Host category: VERTEBRATES
Shell #1Name of element: Capsid / Diameter: 1170 Å / T number(triangulation number): 25

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.6 mg/ml
Buffer solution: 50mM Tris, 150mM NaCl, 2mM CaCl2, 2mM MgCl2
pH: 7.6
Support filmQuantifoil R2/4 holey carbon grids, glow discharged
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 30 % / Method: Blot for 6 seconds before plunging

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Nov 12, 2010 / Details: Low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 310000 X (nominal), 400000 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 300,000 times magnification
Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 2100 nm
Specimen HolderModel: OTHER / Temperature: 90 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1101 / Scanner: OTHER / Sampling size: 15 microns / Bit depth: 16

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: The particles were selected with an in-house script and processed using Frealign
Number of projections: 520 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Fourier methods / Software: Frealign / CTF correction: Each particle / Resolution: 11.1 Å / Resolution method: FSC 0.5

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