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- EMDB-7034: Improved cryoEM structure of human adenovirus type 5 with atomic ... -

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Basic information

Entry
Database: EMDB / ID: 7034
TitleImproved cryoEM structure of human adenovirus type 5 with atomic details of minor proteins VI and VII
SampleHuman adenovirus C serotype 5
SourceHuman adenovirus C serotype 5 / virus
Map datahuman adenovirus type 5
Methodsingle particle reconstruction, at 3.2 Å resolution
AuthorsDai XH / Wu L / Sun R / Zhou ZH
CitationJ. Virol., 2017

J. Virol., 2017 Yorodumi Papers
Atomic Structures of Minor Proteins VI and VII in the Human Adenovirus.
Xinghong Dai / Lily Wu / Ren Sun / Z Hong Zhou

Validation ReportPDB-ID: 6b1t

SummaryFull reportAbout validation report
DateDeposition: Sep 18, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Sep 27, 2017 / Last update: Oct 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6b1t
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6b1t
  • Imaged by Jmol
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_7034.map.gz (map file in CCP4 format, 8388609 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1280 pix
0.85 Å/pix.
= 1088. Å
1280 pix
0.85 Å/pix.
= 1088. Å
1280 pix
0.85 Å/pix.
= 1088. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-11.581982 - 16.747877
Average (Standard dev.)0.004020501 (0.87556183)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128012801280
Origin-640-640-640
Limit639639639
Spacing128012801280
CellA=B=C: 1088 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1088.0001088.0001088.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-640-640-640
NC/NR/NS128012801280
D min/max/mean-11.58216.7480.004

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Supplemental data

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Sample components

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Entire Human adenovirus C serotype 5

EntireName: Human adenovirus C serotype 5 / Details: Cultured in HEK293T cells and purified from media / Number of components: 9
MassTheoretical: 150 MDa

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Component #1: virus, Human adenovirus C serotype 5

VirusName: Human adenovirus C serotype 5 / Class: VIRION / Details: Cultured in HEK293T cells and purified from media / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 150 MDa
SpeciesSpecies: Human adenovirus C serotype 5 / virus
Source (natural)Host Species: Homo sapiens / human
Shell #1Name of element: capsid / Diameter: 900 Å / T number(triangulation number): 25

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Component #2: protein, Hexon protein

ProteinName: Hexon protein / Recombinant expression: No
MassTheoretical: 108.107617 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #3: protein, Penton protein

ProteinName: Penton protein / Recombinant expression: No
MassTheoretical: 63.356602 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #4: protein, Pre-hexon-linking protein IIIa

ProteinName: Pre-hexon-linking protein IIIa / Recombinant expression: No
MassTheoretical: 65.322805 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #5: protein, Pre-hexon-linking protein VIII

ProteinName: Pre-hexon-linking protein VIII / Recombinant expression: No
MassTheoretical: 24.71059 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #6: protein, Hexon-interlacing protein

ProteinName: Hexon-interlacing protein / Recombinant expression: No
MassTheoretical: 14.468134 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #7: protein, Pre-protein VI

ProteinName: Pre-protein VI / Recombinant expression: No
MassTheoretical: 3.584953 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #8: protein, Pre-histone-like nucleoprotein

ProteinName: Pre-histone-like nucleoprotein / Recombinant expression: No
MassTheoretical: 1.198438 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Component #9: protein, Pre-protein VI

ProteinName: Pre-protein VI / Recombinant expression: No
MassTheoretical: 23.460559 kDa
SourceSpecies: Human adenovirus C serotype 5 / virus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 nm / Energy filter: Gatan Image Filter / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80 - K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5608 / Sampling size: 2.5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 53000
3D reconstructionAlgorithm: FOURIER SPACE / Software: eLite3D / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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