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- EMDB-5699: CryoEM structure of EGFR-specific virus (derived from sindbis virus) -

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Basic information

Entry
Database: EMDB / ID: 5699
TitleCryoEM structure of EGFR-specific virus (derived from sindbis virus)
Map dataCryoEM structure of EGFR-specific virus derived from sindbis virus
SampleEGFR-specific virus (derived from sindbis virus):
virus
KeywordsEGFR-specific virus / sindbis virus
Sourcesynthetic construct (EGFR-specific Sindbis virus)
Methodsingle particle reconstruction / cryo EM / 12.2 Å resolution
AuthorsDai H / Liu Z / Jiang W / Kuhn RJ
CitationJournal: J. Virol. / Year: 2013
Title: Directed evolution of a virus exclusively utilizing human epidermal growth factor receptor as the entry receptor.
Authors: Hong-Sheng Dai / Zheng Liu / Wen Jiang / Richard J Kuhn
DateDeposition: Jun 25, 2013 / Header (metadata) release: Aug 28, 2013 / Map release: Jul 30, 2014 / Last update: Oct 12, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5699.map.gz (map file in CCP4 format, 132862 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
324 pix
3.24 Å/pix.
= 1049.76 Å
324 pix
3.24 Å/pix.
= 1049.76 Å
324 pix
3.24 Å/pix.
= 1049.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.24 Å
Density
Contour Level:3.5 (by emdb), 3.5 (movie #1):
Minimum - Maximum-11.02840233 - 21.56969070
Average (Standard dev.)0.49513358 (1.98857570)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions324324324
Origin-162-162-162
Limit161161161
Spacing324324324
CellA=B=C: 1049.76 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.243.243.24
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z1049.7601049.7601049.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-162-162-162
NC/NR/NS324324324
D min/max/mean-11.02821.5700.495

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Supplemental data

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Sample components

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Entire EGFR-specific virus (derived from sindbis virus)

EntireName: EGFR-specific virus (derived from sindbis virus) / Details: The sample was monodisperse. / Number of components: 1 / Oligomeric State: icosahedral

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Component #1: virus, synthetic construct

VirusName: synthetic construct / a.k.a: EGFR-specific Sindbis virus / Class: VIRION
Details: EGF domain was engrafted onto an icosahedral virus scaffold, and directed evolution was conducted to stabilize the chimeric virus.
Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: synthetic construct (EGFR-specific Sindbis virus) / Strain: EGFR-specific no.1
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: E1 and E2-EGF / Diameter: 375.00 Å / T number(triangulation number): 4

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/ml / Buffer solution: 50 mM Tris, 200 mM NaCl, 1 mM EDTA / pH: 7.4
Support film400 mesh copper grid with thin carbon support, glow discharged in air
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 97.15 K / Humidity: 70 % / Method: Blot for 6 seconds before plunging.

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG / Date: Oct 12, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal), 39190 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 5000 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Temperature: 97 K ( 93.15 - 100.15 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 166 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 3.24 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2290
3D reconstructionAlgorithm: projection matching / Software: jspr, EMAN2, EMAN / CTF correction: each particle / Details: Final maps were calculated from 2290 particles. / Resolution: 12.2 Å
Resolution method: FSC at 0.143 cut-off between two independently refined density maps, gold-standard

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Atomic model buiding

Modeling #1Software: veda / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 3J0F
Modeling #2Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 1JL9

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