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- EMDB-49251: Icosahedral capsid assembly of phage JohannRWettstein (Bas63) -

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Basic information

Entry
Database: EMDB / ID: EMD-49251
TitleIcosahedral capsid assembly of phage JohannRWettstein (Bas63)
Map dataIcosahedral capsid assembly of phage JohannRWettstein (Bas63)
Sample
  • Virus: Escherichia phage JohannRWettstein (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Head stabilization/decoration protein
    • Protein or peptide: Immunoglobulin-like domain protein
KeywordsCapsid / Major capsid protein / decoration protein / HOC-like / IG-like / phage / bacteriophage / VIRAL PROTEIN
Function / homology
Function and homology information


cell-cell adhesion / viral capsid / host cell cytoplasm / membrane
Similarity search - Function
Major capsid protein GpE / Phage major capsid protein E / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin-like domain protein / Head stabilization/decoration protein / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage JohannRWettstein (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsHodgkinson-Bean J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: To Be Published
Title: Icosahedral capsid assembly of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean J / Ayala R / McJarrow-Keller K / Cassin L / Rutter GL / Crowe AJM / Wolf M / Bostina M
History
DepositionFeb 16, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49251.png

Downloads & links

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Map

FileDownload / File: emd_49251.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral capsid assembly of phage JohannRWettstein (Bas63)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 756 pix.
= 1048.572 Å		1.39 Å/pix.
x 756 pix.
= 1048.572 Å		1.39 Å/pix.
x 756 pix.
= 1048.572 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.873
Minimum - Maximum-1.407499 - 3.1107688
Average (Standard dev.)0.01391275 (±0.20021078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions756756756
Spacing756756756
CellA=B=C: 1048.572 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49251_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49251_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage JohannRWettstein

EntireName: Escherichia phage JohannRWettstein (virus)
Components
  • Virus: Escherichia phage JohannRWettstein (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Head stabilization/decoration protein
    • Protein or peptide: Immunoglobulin-like domain protein

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Supramolecule #1: Escherichia phage JohannRWettstein

SupramoleculeName: Escherichia phage JohannRWettstein / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2852035 / Sci species name: Escherichia phage JohannRWettstein / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 41.600082 KDa
SequenceString: MLTNSEKSRF FLADLTGEVQ SIPNTYGYIS NLGLFRSAPI TQTTFLMDLT DWDVSLLDAV DRDSRKAETS APERVRQISF PMMYFKEVE SITPDEIQGV RQPGTANELT TEAVVRAKKL MKIRTKFDIT REFLFMQALK GKVVDARGTL YADLYKQFDV E KKTVYFDL ...String:
MLTNSEKSRF FLADLTGEVQ SIPNTYGYIS NLGLFRSAPI TQTTFLMDLT DWDVSLLDAV DRDSRKAETS APERVRQISF PMMYFKEVE SITPDEIQGV RQPGTANELT TEAVVRAKKL MKIRTKFDIT REFLFMQALK GKVVDARGTL YADLYKQFDV E KKTVYFDL DNPNADIDAS IEELRMHMED EAKTGTVING EEIHVVVDRV FFSKLVKHPK IRDAYLAQQT PLAWQQITGS LR TGGTDGV QAHMNTFYYG GVKFVQYNGK FKDKRGKVHT LVSIDSVAAT VGVGHAFPNV SMLGEANNIF EVAYGPCPKM GYA NTLGQE LYVFEYEKDR DEGIDFEAHS YMLPYCTRPQ LLVDVRADAK AD

UniProtKB: Major capsid protein

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Macromolecule #2: Head stabilization/decoration protein

MacromoleculeName: Head stabilization/decoration protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 13.606316 KDa
SequenceString:
MAYQGFTKLG NREPLNDIIL WEQITPTGHS RKEYTPQAST EYRVGEVLKA DGTKVQAGEE AQADSVCIVN FYADLQLSYH GQLKVVGIH RDAELKDLLT LEASVDAAAV KTALAAKGID FVPTGL

UniProtKB: Head stabilization/decoration protein

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Macromolecule #3: Immunoglobulin-like domain protein

MacromoleculeName: Immunoglobulin-like domain protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 48.003848 KDa
SequenceString: MIKAKTYPDF KEFVKGFIAN VKAGKRYDFR TYQEAILPLT YSSYWPEADI AEVEKFDYKP DYKVPFSDDL LYSIGAQMRT SDFFMDLQY AIINGKDVDT VYCEWLARVK PFSMLNAKLK DAIKPPAITQ QPTNQTVNEG GTLTLSVIAT NATGYQWKKG G EDISSATS ...String:
MIKAKTYPDF KEFVKGFIAN VKAGKRYDFR TYQEAILPLT YSSYWPEADI AEVEKFDYKP DYKVPFSDDL LYSIGAQMRT SDFFMDLQY AIINGKDVDT VYCEWLARVK PFSMLNAKLK DAIKPPAITQ QPTNQTVNEG GTLTLSVIAT NATGYQWKKG G EDISSATS ATYTKQSVVP SDAGSYTCVV SGEAGTSVTS DAATVTVNAL PVITQQPSSQ TINEGGNINL EVTATGATGY QW KKDGSDI PSATEATYSK SGALPTDAGS YTCVVTGAGG SVTSSAATVT VNALPVITQQ PTAKTVNEGG TLTLNIVATG ATG YQWSKD NVSIEEAKSA TFTKAGVTPA DAGSYKCTVT GAGGDVVSDA AVVTVNALPV ITQQPTNQEI TEGETLTLNV VATG ATGYQ WKKGEENIPD ATTATYTKEG ATAADAGSYT CVVTGAGGSV TSNAATVTVN PAGGE

UniProtKB: Immunoglobulin-like domain 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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30942
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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