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- EMDB-6000: Full virus map of Brome Mosaic Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-6000
TitleFull virus map of Brome Mosaic Virus
Map datafull BMV map with combined data
Sample
  • Sample: brome mosaic virus
  • Virus: Brome mosaic virus
Function / homologyBromovirus coat protein / Bromovirus coat protein / T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / ribonucleoprotein complex / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Biological speciesBrome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang Z / Hryc FC / Bammes B / Afonine PV / Jakana J / Chen DH / Liu XA / Baker ML / Kao C / Ludtke SJ ...Wang Z / Hryc FC / Bammes B / Afonine PV / Jakana J / Chen DH / Liu XA / Baker ML / Kao C / Ludtke SJ / Schmid MF / Adams PD / Chiu W
CitationJournal: Nat Commun / Year: 2014
Title: An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
Authors: Zhao Wang / Corey F Hryc / Benjamin Bammes / Pavel V Afonine / Joanita Jakana / Dong-Hua Chen / Xiangan Liu / Matthew L Baker / Cheng Kao / Steven J Ludtke / Michael F Schmid / Paul D Adams / Wah Chiu /
Abstract: Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains ...Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.
History
DepositionJul 10, 2014-
Header (metadata) releaseAug 20, 2014-
Map releaseSep 10, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j7l
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j7m
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j7n
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j7l
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j7m
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j7n
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-6000_ima...

Downloads & links

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Map

FileDownload / File: emd_6000.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull BMV map with combined data
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 420 pix.
= 415.8 Å		0.99 Å/pix.
x 420 pix.
= 415.8 Å		0.99 Å/pix.
x 420 pix.
= 415.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 5.0 / Movie #1: 4
Minimum - Maximum-10.33948612 - 17.469449999999998
Average (Standard dev.)0.00000003 (±1.11417329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 415.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.990.990.99
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z415.800415.800415.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-10.33917.4690.000

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Supplemental data

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Supplemental map: emd 6000 additional 1.map

Fileemd_6000_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6000 additional 2.map

Fileemd_6000_additional_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Supplemental map: emd 6000 additional 3.map

Fileemd_6000_additional_3.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6000 additional 4.map

Fileemd_6000_additional_4.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 6000 additional 5.map

Fileemd_6000_additional_5.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 : brome mosaic virus

EntireName: brome mosaic virus
Components
  • Sample: brome mosaic virus
  • Virus: Brome mosaic virus

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Supramolecule #1000: brome mosaic virus

SupramoleculeName: brome mosaic virus / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 4.6 MDa

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Supramolecule #1: Brome mosaic virus

SupramoleculeName: Brome mosaic virus / type: virus / ID: 1 / NCBI-ID: 12302 / Sci species name: Brome mosaic virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Triticum aestivum (bread wheat) / synonym: PLANTAE(HIGHER PLANTS)

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 171.0 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
DateJan 10, 2013
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: MPSA, EMAN / Number images used: 30000

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