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- EMDB-1016: Difference imaging of adenovirus: bridging the resolution gap bet... -

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Basic information

Entry
Database: EMDB / ID: EMD-1016
TitleDifference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy.
Map dataAdeno-virus type 2.
Sample
  • Sample: adenovirus type 2
  • Virus: Human adenovirus 2
Biological speciesHuman adenovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsStewart PL / Fuller SD / Burnett RM
CitationJournal: EMBO J / Year: 1993
Title: Difference imaging of adenovirus: bridging the resolution gap between X-ray crystallography and electron microscopy.
Authors: P L Stewart / S D Fuller / R M Burnett /
Abstract: While X-ray crystallography provides atomic resolution structures of proteins and small viruses, electron microscopy provides complementary structural information on the organization of larger ...While X-ray crystallography provides atomic resolution structures of proteins and small viruses, electron microscopy provides complementary structural information on the organization of larger assemblies at lower resolution. A novel combination of these two techniques has bridged this resolution gap and revealed the various structural components forming the capsid of human type 2 adenovirus. An image reconstruction of the intact virus, derived from cryo-electron micrographs, was deconvolved with an approximate contrast transfer function to mitigate microscope distortions. A model capsid was calculated from 240 copies of the crystallographic structure of the major capsid protein and filtered to the correct resolution. Subtraction of the calculated capsid from the corrected reconstruction gave a three-dimensional difference map revealing the minor proteins that stabilize the virion. Elongated density penetrating the hexon capsid at the facet edges was ascribed to polypeptide IIIa, a component required for virion assembly. Density on the inner surface of the capsid, connecting the ring of peripentonal hexons, was assigned as polypeptide VI, a component that binds DNA. Identification of the regions of hexon that contact the penton base suggests a structural mechanism for previously proposed events during cell entry.
History
DepositionOct 15, 2002-
Header (metadata) releaseOct 15, 2002-
Map releaseOct 15, 2002-
UpdateFeb 27, 2013-
Current statusFeb 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 138
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 138
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1016.gif

emd_1016.tif

emd_emd_1016...

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Map

FileDownload / File: emd_1016.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationAdeno-virus type 2.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
7.3 Å/pix.
x 161 pix.
= 1175.3 Å		7.3 Å/pix.
x 161 pix.
= 1175.3 Å		7.3 Å/pix.
x 161 pix.
= 1175.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 148.0 / Movie #1: 138
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)112.588562010000004 (±18.983009339999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions161161161
Spacing161161161
CellA=B=C: 1175.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z7.37.37.3
M x/y/z161161161
origin x/y/z0.0000.0000.000
length x/y/z1175.3001175.3001175.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS161161161
D min/max/mean0.000255.000112.589

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Supplemental data

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Supplemental map: emd 1016 additional 1.map

Fileemd_1016_additional_1.map
Projections & Slices
AxesZYX

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Supplemental map: emd 1016 additional 2.map

Fileemd_1016_additional_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 1016 additional 3.map

Fileemd_1016_additional_3.map
Projections & Slices
AxesZYX

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Sample components

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Entire : adenovirus type 2

EntireName: adenovirus type 2
Components
  • Sample: adenovirus type 2
  • Virus: Human adenovirus 2

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Supramolecule #1000: adenovirus type 2

SupramoleculeName: adenovirus type 2 / type: sample / ID: 1000 / Oligomeric state: T=25 particle / Number unique components: 1
Molecular weightTheoretical: 150 MDa

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Supramolecule #1: Human adenovirus 2

SupramoleculeName: Human adenovirus 2 / type: virus / ID: 1 / NCBI-ID: 10515 / Sci species name: Human adenovirus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: fibres (5f positions) 1090A / T number (triangulation number): 25
Virus shellShell ID: 2 / Name: capsid (along 2f) 884A / T number (triangulation number): 1

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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

Concentration10 mg/mL
BufferpH: 7.4
Details: Sample stored in CsCl was diluted in Tris (10mM) NaCl (100 mM) pH 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 23 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: EMBL plunger. plunging at ambient temperature and humidity
Method: Blot for 2 sec

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Electron microscopy

MicroscopeFEI/PHILIPS EM400
TemperatureAverage: 105 K
DetailsDetails of the microscopy are in Stewart, P. L., Burnett, R. M., Cyrklaff, M. and Fuller, S. D. (1991). Image reconstruction reveals the complex molecular organization of adenovirus. Cell 67, 145-54. Images were taken in triples at 1, 2.6 and 8.8 microns underfocus. Some images were taken at 12 degrees tilt to compensate for the preference for the virus to orient with the fibres away from the water layer. For image reconstruction see: Stewart, P. L., Burnett, R. M.,Cyrklaff, M. and Fuller, S. D. (1991). Image reconstruction reveals the complex molecular organization of adenovirus. Cell 67, 145-54. For reconstruction details see: P.L. Stewart, S.D. Fuller, R. M. Burnett, (1993). Difference imaging of adenovirus: bridging the resolution gap between X- ray crystallography and electron microscopy EMBO J.Stewart PL, Burnett RM. Adenovirus structure by X-ray crystallography and electron microscopy. Curr Top Microbiol Immunol. 1995, 199 (1):25-38. The PDB code for the Ad2 hexon model is 1DHX, and the reference Athappilly, F. K., Murali, R., Rux, J. J., Cai, Z., Burnett, R. M.: The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution. J Mol Biol 242 pp. 430 (1994)
DateJan 1, 1990
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OPTRONICS / Digitization - Sampling interval: 25 µm / Number real images: 50 / Average electron dose: 8 e/Å2 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 80 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 8.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 34000
Sample stageSpecimen holder: eucentric - Philips EM400 / Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 12

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Image processing

DetailsPurified by centrifugation in CsCl
CTF correctionDetails: initially different defocuses were combined by summing in resolution bands
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMBL-ICOS / Number images used: 29
Final angle assignmentDetails: sufficient to give maximum inverse eigenvalue of 0.1

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Atomic model buiding 1

SoftwareName: maximizing cross correlation
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 3000 / Target criteria: max cross correlation

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