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- EMDB-28820: phi-29 prohead MCP gp8 penton maturation intermediate, with assoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-28820
Titlephi-29 prohead MCP gp8 penton maturation intermediate, with associated scaffold gp7 tetramer
Map dataPhi-29 prohead MCP gp8 penton maturation intermediate, with associated scaffold gp7 tetramer
Sample
  • Virus: Bacillus phage phi29 (virus)
    • Protein or peptide: bacteriophage phi-29 major capsid protein gp 8
    • Protein or peptide: bacteriophage phi-29 scaffolding protein gp 7
Keywordsbacteriophage / prohead / scaffold / HK97 fold / VIRUS
Function / homology
Function and homology information


viral scaffold / viral procapsid / T=3 icosahedral viral capsid / virion assembly / DNA binding
Similarity search - Function
Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Capsid assembly scaffolding protein / Major capsid protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWoodson ME / Morais MC / Jardine PJ / Zhang W / Prokhorov NS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122979 United States
CitationJournal: To Be Published
Title: Scaffold Oligomers Control Prohead Expansion
Authors: Woodson ME / Morais MC / Prokhorov NS / Scott SD / Zhang W / Choi KH / Jardine PJ
History
DepositionNov 8, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28820.png

Downloads & links

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Map

FileDownload / File: emd_28820.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhi-29 prohead MCP gp8 penton maturation intermediate, with associated scaffold gp7 tetramer
Voxel sizeX=Y=Z: 1.272 Å
Density
Contour LevelBy AUTHOR: 0.0251
Minimum - Maximum-0.01805469 - 0.058145694
Average (Standard dev.)-0.0008428673 (±0.0046570404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 228.95999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_28820_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_28820_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus phage phi29

EntireName: Bacillus phage phi29 (virus)
Components
  • Virus: Bacillus phage phi29 (virus)
    • Protein or peptide: bacteriophage phi-29 major capsid protein gp 8
    • Protein or peptide: bacteriophage phi-29 scaffolding protein gp 7

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2884424 / Sci species name: Bacillus phage phi29 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Bacillus subtilis (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 35.0 Å / T number (triangulation number): 3

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Macromolecule #1: bacteriophage phi-29 major capsid protein gp 8

MacromoleculeName: bacteriophage phi-29 major capsid protein gp 8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRI GLVVIRQVSL NNPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV F EREMPNVK TLFHERNRQG FYHQTIQDDS LKTAFVSWGN FESFVSSIIN ...String:
MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRI GLVVIRQVSL NNPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV F EREMPNVK TLFHERNRQG FYHQTIQDDS LKTAFVSWGN FESFVSSIIN AIYNSAEVDE YE YMKLLVD NYYSKGLFTT VKIDEPTSST GALTEFVKKM RATARKLTLP QGSRDWNSMA VRT RSYMED LHLIIDADLE AELDVDVLAK AFNMNRTDFL GNVTVIDGFA STGLEAVLVD KDWF MVYDN LHKMETVRNP RGLYWNYYYH VWQTLSVSRF ANAVAFVSGD VPAVTQVIVS PNIAA VKQG GQQQFTAYVR ATNAKDHKVV WSVEGGSTGT AITGDGLLSV SGNEDNQLTV KATVDI GTE DKPKLVVGEA VVSIRPNNAS GGAQA

UniProtKB: Major capsid protein

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Macromolecule #2: bacteriophage phi-29 scaffolding protein gp 7

MacromoleculeName: bacteriophage phi-29 scaffolding protein gp 7 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString:
MPLKPEEHED ILNKLLDPEL AQSERTEALQ QLRVNYGSFV SEYNDLTKSH EKLAAEKDDL IVSNSKLFR QIGLTDKQEE DHKKADISET ITIEDLEAK

UniProtKB: Capsid assembly scaffolding 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: 7.8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
5.0 mMMgCl2magnesium chloride
50.0 mMNaClSodium chloridesodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 98000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 5593 / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 52655
Startup modelType of model: OTHER / Details: density from full capsid extracted with 'segger'
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 500000 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 204500

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER

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