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- EMDB-4098: Cryo-EM reconstruction of bacteriophage AP205 virus-like particles -

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Basic information

Entry
Database: EMDB / ID: EMD-4098
TitleCryo-EM reconstruction of bacteriophage AP205 virus-like particles
Map dataBacteriophage AP205 cryo-EM map
SampleAP205 != Acinetobacter phage AP205

AP205

  • Virus: Acinetobacter phage AP205 (virus)
    • Protein or peptide: Coat protein
KeywordsRNA bacteriophage / Leviviridae / coat protein / virus-like particle / VIRUS LIKE PARTICLE
Function / homology: / AP205 coat protein / viral capsid / Coat protein
Function and homology information
Biological speciesAcinetobacter phage AP205 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsDiebolder CA / Rumnieks J
CitationJournal: J Mol Biol / Year: 2016
Title: Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages.
Authors: Mihails Shishovs / Janis Rumnieks / Christoph Diebolder / Kristaps Jaudzems / Loren B Andreas / Jan Stanek / Andris Kazaks / Svetlana Kotelovica / Inara Akopjana / Guido Pintacuda / Roman I ...Authors: Mihails Shishovs / Janis Rumnieks / Christoph Diebolder / Kristaps Jaudzems / Loren B Andreas / Jan Stanek / Andris Kazaks / Svetlana Kotelovica / Inara Akopjana / Guido Pintacuda / Roman I Koning / Kaspars Tars /
Abstract: AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus- ...AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.
History
DepositionAug 17, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseDec 14, 2016-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lqp
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lqp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4098.png

Downloads & links

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Map

FileDownload / File: emd_4098.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage AP205 cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å		1.34 Å/pix.
x 400 pix.
= 536. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.012 / Movie #1: 0.014
Minimum - Maximum-0.026991447 - 0.053230528
Average (Standard dev.)0.000009012775 (±0.0041545494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 536.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0270.0530.000

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Supplemental data

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Sample components

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Entire : AP205

EntireName: AP205
Components
  • Virus: Acinetobacter phage AP205 (virus)
    • Protein or peptide: Coat protein

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Supramolecule #1: Acinetobacter phage AP205

SupramoleculeName: Acinetobacter phage AP205 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 154784 / Sci species name: Acinetobacter phage AP205 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage AP205 (virus)
Molecular weightTheoretical: 13.820569 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ANKPMQPITS TANKIVWSDP TRLSTTFSAS LLRQRVKVGI AELNNVSGQY VSVYKRPAPK PEGCADACVI MPNENQSIRT VISGSAENL ATLKAEWETH KRNVDTLFAS GNAGLGFLDP TAAIVSSDTT

UniProtKB: Coat protein

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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

BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: FEI SFEG
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 63253
Startup modelType of model: NONE / Details: xmipp ransac
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Xmipp / Number images used: 2215
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp
Final 3D classificationSoftware - Name: Xmipp
FSC plot (resolution estimation)

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