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- EMDB-10091: Granulovirus occlusion bodies by serial electron diffraction -

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Basic information

Entry
Database: EMDB / ID: EMD-10091
TitleGranulovirus occlusion bodies by serial electron diffraction
Map data
Sample
  • Virus: Cydia pomonella granulosis virus (isolate Mexican)
    • Protein or peptide: Granulin
  • Ligand: water
Keywordsgranulovirus / occlusion body / serial crystallography / viral protein
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCydia pomonella granulosis virus (isolate Mexico/1963) / Cydia pomonella granulosis virus (isolate Mexican)
Methodelectron crystallography / cryo EM / Resolution: 1.6 Å
AuthorsBuecker R / Mehrabi P
CitationJournal: Nat Commun / Year: 2020
Title: Serial protein crystallography in an electron microscope.
Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / ...Authors: Robert Bücker / Pascal Hogan-Lamarre / Pedram Mehrabi / Eike C Schulz / Lindsey A Bultema / Yaroslav Gevorkov / Wolfgang Brehm / Oleksandr Yefanov / Dominik Oberthür / Günther H Kassier / R J Dwayne Miller /
Abstract: Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample ...Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
History
DepositionJun 21, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s2o
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10091.png

Downloads & links

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Map

FileDownload / File: emd_10091.map.gz / Format: CCP4 / Size: 41.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.38 Å/pix.
x 253 pix.
= 96.697 Å		0.38 Å/pix.
x 226 pix.
= 86.377 Å		0.38 Å/pix.
x 190 pix.
= 72.618 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.3822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.8132585 - 6.5377893
Average (Standard dev.)0.008455574 (±0.25972122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-26-84-166
Dimensions226190253
Spacing190226253
CellA: 72.618004 Å / B: 86.3772 Å / C: 96.6966 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.38220.382199115044250.38220158102767
M x/y/z190226253
origin x/y/z0.0000.0000.000
length x/y/z72.61886.37796.697
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-84-26-166
NC/NR/NS190226253
D min/max/mean-1.8136.5380.008

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Supplemental data

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Sample components

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Entire : Cydia pomonella granulosis virus (isolate Mexican)

EntireName: Cydia pomonella granulosis virus (isolate Mexican)
Components
  • Virus: Cydia pomonella granulosis virus (isolate Mexican)
    • Protein or peptide: Granulin
  • Ligand: water

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Supramolecule #1: Cydia pomonella granulosis virus (isolate Mexican)

SupramoleculeName: Cydia pomonella granulosis virus (isolate Mexican) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 654905
Sci species name: Cydia pomonella granulosis virus (isolate Mexican)
Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Granulin

MacromoleculeName: Granulin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cydia pomonella granulosis virus (isolate Mexico/1963)
Strain: isolate Mexico/1963
Molecular weightTheoretical: 29.378559 KDa
Recombinant expressionOrganism: Cydia pomonella granulosis virus (isolate Mexican)
SequenceString: MGYNKSLRYS RHDGTSCVID NHHLKSLGAV LNDVRRKKDR IREAEYEPII DIADQYMVTE DPFRGPGKNV RITLFKEIRR VHPDTMKLV CNWSGKEFLR ETWTRFISEE FPITTDQEIM DLWFELQLRP MHPNRCYKFT MQYALGAHPD YVAHDVIRQQ D PYYVGPNN ...String:
MGYNKSLRYS RHDGTSCVID NHHLKSLGAV LNDVRRKKDR IREAEYEPII DIADQYMVTE DPFRGPGKNV RITLFKEIRR VHPDTMKLV CNWSGKEFLR ETWTRFISEE FPITTDQEIM DLWFELQLRP MHPNRCYKFT MQYALGAHPD YVAHDVIRQQ D PYYVGPNN IERINLSKKG FAFPLTCLQS VYNDNFERFF DDVLWPYFYR PLVYVGTTSA EIEEIMIEVS LLFKIKEFAP DV PLFTGPA Y

UniProtKB: Granulin

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 90 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 93.0 K / Max: 100.0 K
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 1536 pixel / Digitization - Dimensions - Height: 512 pixel / Number grids imaged: 1 / Number diffraction images: 32000 / Average exposure time: 0.01 sec. / Average electron dose: 4.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 5.0 µm / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Camera length: 2580 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN / Tilt angle: 0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: Coot
Molecular replacementSoftware - Name: PHENIX (ver. 1.17)
Merging software listSoftware - details: CrystFEL
Crystallography statisticsNumber intensities measured: 9650574 / Number structure factors: 23422 / Fourier space coverage: 100 / R sym: 0.093 / R merge: 0.093 / Overall phase error: 13.64 / Overall phase residual: 1 / Phase error rejection criteria: 0 / High resolution: 1.6 Å / Shell - Shell ID: 1 / Shell - High resolution: 10.0 Å / Shell - Low resolution: 1.55 Å / Shell - Number structure factors: 1 / Shell - Phase residual: 1 / Shell - Fourier space coverage: 1 / Shell - Multiplicity: 1

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Atomic model buiding 1

Initial modelPDB ID:

5g0z


Chain - Chain ID: A / Chain - Residue range: 6-248 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6s2o:
Granulovirus occlusion bodies by serial electron diffraction

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