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- EMDB-62058: 5-fold vertex of SH-Ab15497 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62058
Title5-fold vertex of SH-Ab15497
Map data
Sample
  • Virus: Acinetobacter phage SH-Ab 15497 (virus)
    • Protein or peptide: Major capsid protein
Keywordscapsid / VIRAL PROTEIN
Function / homologyMajor capsid protein 13-like / Major capsid protein 13-like / Major capsid protein
Function and homology information
Biological speciesAcinetobacter phage SH-Ab 15497 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLin J / Zhao SW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370704 China
National Natural Science Foundation of China (NSFC)32122024 China
CitationJournal: To Be Published
Title: 5-fold vertex of SH-Ab15497
Authors: Lin J / Zhao SW
History
DepositionOct 21, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62058.png

Downloads & links

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Map

FileDownload / File: emd_62058.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.07635178 - 0.124152616
Average (Standard dev.)-0.0002736496 (±0.0051814364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62058_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62058_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Acinetobacter phage SH-Ab 15497

EntireName: Acinetobacter phage SH-Ab 15497 (virus)
Components
  • Virus: Acinetobacter phage SH-Ab 15497 (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Acinetobacter phage SH-Ab 15497

SupramoleculeName: Acinetobacter phage SH-Ab 15497 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2060946 / Sci species name: Acinetobacter phage SH-Ab 15497 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Diameter: 650.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage SH-Ab 15497 (virus)
Molecular weightTheoretical: 34.20616 KDa
SequenceString: MALSDLQVFN DWAYKTMSEV LDQQVELFNG ATRGAIILRS AGNTGDLSEA AFWAKIQGLV RPRDPYSNAD VAAKDLRQLV DNTIKVASG TPPINIPPSM LRWIQKNPQE AGAVIGQQLA GDTMQDMLNN GLAAGKAAFT AGGAVHDISA AGTGLMTQRA F NAAQRIFG ...String:
MALSDLQVFN DWAYKTMSEV LDQQVELFNG ATRGAIILRS AGNTGDLSEA AFWAKIQGLV RPRDPYSNAD VAAKDLRQLV DNTIKVASG TPPINIPPSM LRWIQKNPQE AGAVIGQQLA GDTMQDMLNN GLAAGKAAFT AGGAVHDISA AGTGLMTQRA F NAAQRIFG DRSTDIQVWV SHSSPLFDLY DNALANAEQL YVFGTVNVRA DAFGRPIIIT DSPALVSGAA ETLRHSTLGL TT GAILIEQ NQDFDSTVVD GTGKQNITRQ YQAEWSYNLG VNGYAYDIAT GGKAPNPTAL ATAANWDKIS TSIKDTGGVV LVT K

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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 27057 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: De novo SGD model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266059
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Avg.num./class: 14873
FSC plot (resolution estimation)

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