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- EMDB-11013: Localized reconstruction of human adenovirus D26 hexon type 4 -

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Basic information

Entry
Database: EMDB / ID: EMD-11013
TitleLocalized reconstruction of human adenovirus D26 hexon type 4
Map dataLocalized reconstruction of human adenovirus D26 hexon 4
Sample
  • Complex: Adenovirus hexon type 4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuiskonen JT / Abrishami V
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)649053European Union
Wellcome Trust109135/Z/15/A United Kingdom
CitationJournal: Prog Biophys Mol Biol / Year: 2021
Title: Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data.
Authors: Vahid Abrishami / Serban L Ilca / Josue Gomez-Blanco / Ilona Rissanen / José Miguel de la Rosa-Trevín / Vijay S Reddy / José-Maria Carazo / Juha T Huiskonen /
Abstract: Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM ...Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.
History
DepositionMay 6, 2020-
Header (metadata) releaseJun 10, 2020-
Map releaseJun 10, 2020-
UpdateMar 24, 2021-
Current statusMar 24, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11013.png

Downloads & links

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Map

FileDownload / File: emd_11013.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalized reconstruction of human adenovirus D26 hexon 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å		1.31 Å/pix.
x 256 pix.
= 335.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.09911038 - 0.14872397
Average (Standard dev.)0.0002983528 (±0.010138017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0990.1490.000

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Supplemental data

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Mask #1

Fileemd_11013_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 1 of human adenovirus D26 hexon 4 map

Fileemd_11013_half_map_1.map
AnnotationHalf 1 of human adenovirus D26 hexon 4 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2 of human adenovirus D26 hexon 4 map

Fileemd_11013_half_map_2.map
AnnotationHalf 2 of human adenovirus D26 hexon 4 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adenovirus hexon type 4

EntireName: Adenovirus hexon type 4
Components
  • Complex: Adenovirus hexon type 4

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Supramolecule #1: Adenovirus hexon type 4

SupramoleculeName: Adenovirus hexon type 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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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

Concentration6 mg/mL
BufferpH: 8.1
Component:
ConcentrationFormulaName
40.0 mMTristrisaminomethane
300.0 mMNaClsodium chloride
10.0 mMCaCl2calcium chloride
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 7-38 / Number real images: 2000 / Average exposure time: 7.6 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 69590
Details: A total of 521,040 sub-particle images were extracted from 8,684 particle images.
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.8)
Startup modelType of model: OTHER / Details: Localized reconstruction of the hexon-4
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 521040
Initial angle assignmentType: OTHER / Software - Name: Scipion / Software - details: Localized reconstruction
Details: Orientation parameters were calculated by localized reconstruction from the alignment of the capsid
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Software - details: custom option was added to relax C5 symmetry
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5tx1

chain_id: J

5tx1

chain_id: K

5tx1

chain_id: L
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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