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- EMDB-5156: Bovine Papillomavirus Type 1 (BPV1) cryo-EM reconstruction of L1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5156
TitleBovine Papillomavirus Type 1 (BPV1) cryo-EM reconstruction of L1 pentamer at 3.6A resolution after additional 6-fold NCS averaging within the icosahedral asymmetric unit.
Map dataThis map is a result of additional 6-fold NCS averaging within the ASU. It shows the invariable part of the L1 pentamer and contains the core domain plus parts of the inter-pentamer C-terminal arm interface.
Sample
  • Sample: Bovine Papillomavirus Type 1 (BPV1), full virion
  • Virus: Bovine papillomavirus type 1
Keywordsbovine papillomavirus BPV1 / major capsid protein L1 / single particle cryo-EM / high resolution / cervical cancer
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesBovine papillomavirus type 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWolf M / Garcea RL / Grigorieff N / Harrison SC
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Subunit interactions in bovine papillomavirus.
Authors: Matthias Wolf / Robert L Garcea / Nikolaus Grigorieff / Stephen C Harrison /
Abstract: Papillomaviruses, members of a group of dsDNA viruses associated with epithelial growths and tumors, have compact capsids assembled from 72 pentamers of the protein L1. We have determined the ...Papillomaviruses, members of a group of dsDNA viruses associated with epithelial growths and tumors, have compact capsids assembled from 72 pentamers of the protein L1. We have determined the structure of bovine papillomavirus by electron cryomicrosopy (cryoEM), at approximately 3.6 A resolution. The density map, obtained from single-particle analysis of approximately 4,000 particle images, shows the trace of the L1 polypeptide chain and reveals how the N- and C-terminal "arms" of a subunit (extensions from its beta-jelly-roll core) associate with a neighboring pentamer. Critical contacts come from the C-terminal arm, which loops out from the core of the subunit, forms contacts (including a disulfide) with two subunits in a neighboring pentamer, and reinserts into the pentamer from which it emanates. This trace corrects one feature of an earlier model. We discuss implications of the structure for virion assembly and for pathways of infectious viral entry. We suggest that it should be possible to obtain image reconstructions of comparable resolution from cryoEM images of asymmetric particles. From the work on papillomavirus described here, we estimate that such a reconstruction will require about 1.5 million images to achieve the same number of averaged asymmetric units; structural variability will increase this number substantially.
History
DepositionDec 15, 2009-
Header (metadata) releaseJan 22, 2010-
Map releaseJan 22, 2010-
UpdateApr 28, 2010-
Current statusApr 28, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyj
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5156_1.png

Downloads & links

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Map

FileDownload / File: emd_5156.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map is a result of additional 6-fold NCS averaging within the ASU. It shows the invariable part of the L1 pentamer and contains the core domain plus parts of the inter-pentamer C-terminal arm interface.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 119 pix.
= 633.344 Å		1.24 Å/pix.
x 122 pix.
= 633.344 Å		1.24 Å/pix.
x 118 pix.
= 633.344 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: 1.237 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2 / Movie #1: 1.5
Minimum - Maximum-3.02127 - 5.7926
Average (Standard dev.)0.0812812 (±0.426443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin43-58108
Dimensions122118119
Spacing122118119
CellA=B=C: 633.344 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2371.2371.237
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z633.344633.344633.344
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-5843108
NC/NR/NS118122119
D min/max/mean-3.0215.7930.081

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Supplemental data

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Sample components

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Entire : Bovine Papillomavirus Type 1 (BPV1), full virion

EntireName: Bovine Papillomavirus Type 1 (BPV1), full virion
Components
  • Sample: Bovine Papillomavirus Type 1 (BPV1), full virion
  • Virus: Bovine papillomavirus type 1

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Supramolecule #1000: Bovine Papillomavirus Type 1 (BPV1), full virion

SupramoleculeName: Bovine Papillomavirus Type 1 (BPV1), full virion / type: sample / ID: 1000 / Details: theoretical MM for L1 only / Oligomeric state: T7D icosahedral assembly / Number unique components: 1
Molecular weightTheoretical: 19.4 MDa

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Supramolecule #1: Bovine papillomavirus type 1

SupramoleculeName: Bovine papillomavirus type 1 / type: virus / ID: 1 / Name.synonym: BPV1 / NCBI-ID: 10559 / Sci species name: Bovine papillomavirus type 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: BPV1
Host (natural)Organism: Bos taurus (cattle) / synonym: VERTEBRATES
Molecular weightTheoretical: 19.4 MDa
Virus shellShell ID: 1 / Name: L1 / Diameter: 600 Å / T number (triangulation number): 7

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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

Concentration1.5 mg/mL
BufferpH: 6.2 / Details: 20mM Tris pH6.2, 100mM NaCl, 0.5mM CaCl2
GridDetails: quantifoil CF-1/2-4C
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 70 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: manual plunger. vitrification carried out in cold room.
Method: blot 3.5ul at 4C for 25sec from carbon side with Whatman Nr.40

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 77 K / Max: 77 K / Average: 77 K
Alignment procedureLegacy - Astigmatism: obj lens astig was corrected at 700,000x
Detailsobj aperture cutoff at 2.4A
DateDec 7, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 49 / Average electron dose: 25 e/Å2 / Details: combination of 3 channels / Od range: 1.4 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56588 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder: side entry, eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: ctfilt3 with individual particle adjustment
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: frealign
Details: This map was 6-fold (NCS)averaged within the icosahedral ASU. Ewald sphere correction.
Number images used: 3997

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Atomic model buiding 1

Initial modelPDB ID:

1dzl

SoftwareName: CNSsolve
DetailsProtocol: see 3D-fitting details. SigmaF and phase FOM were estimated from two halfset reconstructions (see publication). Refinement within the resolution range 15-3.5A. Isotropic B-factor correction, automatic bulk solvent parameter search, bulk-solvent correction, coordinate refinement by energy minimization, restrained individual B-factor refinement and unrestrained group B-factor refinement. Both icosahedaral and non-icosahedral capsid symmetry (NCS) were imposed, using icosahedral constraints and six-fold NCS restraints within the asymmetric unit defined in five NCS groups. We used default x-ray scattering factors and a maximum likelihood refinement target (MLHL) with amplitude and phase probability distribution.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 114
Target criteria: MLHL target with ampl. and phase probability distribution
Output model

PDB-3iyj:
Bovine papillomavirus type 1 outer capsid

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