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- EMDB-28824: Phi-29 expanded, DNA-packaged fiberless prohead -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28824
TitlePhi-29 expanded, DNA-packaged fiberless prohead
Map dataPhi-29 expanded, DNA-packaged fiberless prohead
Sample
  • Virus: Bacillus phage phi29 (virus)
    • Protein or peptide: Major capsid protein
Keywordsbacteriophage / prohead / HK97 fold / VIRUS
Function / homologyviral procapsid / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / T=3 icosahedral viral capsid / Major capsid protein
Function and homology information
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWoodson ME / Morais MC / Jardine PJ / Zhang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122979 United States
CitationJournal: Sci Adv / Year: 2025
Title: Phi29 assembly intermediates reveal how scaffold interactions with capsid protein drive capsid construction and maturation
Authors: Woodson M / Prokhorov NS / Scott SD / Zhao W / Zhang W / Choi KH / Jardine PJ / Morais MC
History
DepositionNov 8, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28824.png

Downloads & links

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Map

FileDownload / File: emd_28824.map.gz / Format: CCP4 / Size: 953.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhi-29 expanded, DNA-packaged fiberless prohead
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 630 pix.
= 674.1 Å		1.07 Å/pix.
x 630 pix.
= 674.1 Å		1.07 Å/pix.
x 630 pix.
= 674.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.098080635 - 0.1823762
Average (Standard dev.)0.0006703175 (±0.012086304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions630630630
Spacing630630630
CellA=B=C: 674.10004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 1

Fileemd_28824_half_map_1.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_28824_half_map_2.map
Annotationhalf 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: Major capsid protein

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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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 47 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage phi29 (virus)
Molecular weightTheoretical: 49.894906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRIG LVVIRQVSLN NPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV FEREMPNVKT LFHERNRQGF YHQTIQDDSL KTAFVSWGNF E SFVSSIIN ...String:
MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRIG LVVIRQVSLN NPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV FEREMPNVKT LFHERNRQGF YHQTIQDDSL KTAFVSWGNF E SFVSSIIN AIYNSAEVDE YEYMKLLVDN YYSKGLFTTV KIDEPTSSTG ALTEFVKKMR ATARKLTLPQ GSRDWNSMAV RT RSYMEDL HLIIDADLEA ELDVDVLAKA FNMNRTDFLG NVTVIDGFAS TGLEAVLVDK DWFMVYDNLH KMETVRNPRG LYW NYYYHV WQTLSVSRFA NAVAFVSGDV PAVTQVIVSP NIAAVKQGGQ QQFTAYVRAT NAKDHKVVWS VEGGSTGTAI TGDG LLSVS GNEDNQLTVK ATVDIGTEDK PKLVVGEAVV SIRPNNASGG AQA

UniProtKB: Major capsid 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 chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 5593 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
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: 89000
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: used emdb-6560
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 53000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 53000 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8f2o:
Phi-29 expanded, DNA-packaged fiberless prohead

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