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- EMDB-38202: Major tail protein of SH-Ab15497 -

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Basic information

Entry
Database: EMDB / ID: EMD-38202
TitleMajor tail protein of SH-Ab15497
Map data
Sample
  • Virus: Acinetobacter phage SH-Ab 15497 (virus)
    • Protein or peptide: Major tail structural protein
Keywordshelical reconstruction / C3 symmetry / VIRAL PROTEIN
Function / homologyPhage tail tube protein-like / Phage tail tube protein / Major tail structural protein
Function and homology information
Biological speciesAcinetobacter phage SH-Ab 15497 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 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: Major tail protein of SH-Ab15497
Authors: Lin J / Zhao SW
History
DepositionDec 5, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38202.png

Downloads & links

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Map

FileDownload / File: emd_38202.map.gz / Format: CCP4 / Size: 32.4 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 204 pix.
= 269.28 Å		1.32 Å/pix.
x 204 pix.
= 269.28 Å		1.32 Å/pix.
x 204 pix.
= 269.28 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: 0.025
Minimum - Maximum-0.057306066 - 0.11165621
Average (Standard dev.)0.0006873564 (±0.0066491794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions204204204
Spacing204204204
CellA=B=C: 269.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38202_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_38202_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 tail structural 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 tail structural protein

MacromoleculeName: Major tail structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage SH-Ab 15497 (virus)
Molecular weightTheoretical: 33.208465 KDa
SequenceString: MSDGSRHSMH QVLETVYGEV PATPAFKRIR HNSTTLATAI NTLTSEELRP DRNSMGIRHG TRQVGGEIVS ELSFESLDDT LEALMCGTW NADALVNGVT RRSFSILRQF NDLTSASLPN FVYVGCEYNT MTLSITTEAI VMATFGIVGM NQLEPSSTVP T GATFVEAP ...String:
MSDGSRHSMH QVLETVYGEV PATPAFKRIR HNSTTLATAI NTLTSEELRP DRNSMGIRHG TRQVGGEIVS ELSFESLDDT LEALMCGTW NADALVNGVT RRSFSILRQF NDLTSASLPN FVYVGCEYNT MTLSITTEAI VMATFGIVGM NQLEPSSTVP T GATFVEAP TTEPMDSFTG HVKEGLADIA VATELELQIE NGIAPRYVIG SKKSIKQSIG RFKVSGTLTA YFEDATLVGK FL REEASSL EFVVTDGLAG NSYKFELPKI KYTGGQPDVG GEGPITLSMP FVAEYDPTIL GTLKITRIGA

UniProtKB: Major tail structural protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
8.0 mMMgSO4magnesium sulfate
50.0 mMTris-HCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 38.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 40.7 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 157605
Startup modelType of model: OTHER / Details: De novo SGD model
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8xan:
Major tail protein of SH-Ab15497

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