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- EMDB-38211: Portal protein of SH-Ab15497 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38211
TitlePortal protein of SH-Ab15497
Map data
Sample
  • Virus: Acinetobacter phage SH-Ab 15497 (virus)
    • Protein or peptide: Portal protein
Keywordsdodecamer / DNA channel / VIRAL PROTEIN
Function / homologyDomain of unknown function DUF4055 / Domain of unknown function (DUF4055) / Portal protein
Function and homology information
Biological speciesAcinetobacter phage SH-Ab 15497 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLin J / Zhao SW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370704 China
CitationJournal: To Be Published
Title: Portal 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_38211.png

Downloads & links

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Map

FileDownload / File: emd_38211.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 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: 0.012
Minimum - Maximum-0.050044037 - 0.078151986
Average (Standard dev.)-0.00002168481 (±0.0041695074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38211_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_38211_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: Portal 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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter phage SH-Ab 15497 (virus)
Molecular weightTheoretical: 57.059113 KDa
SequenceString: MRDSNNIKYV REDAKKMHKL WAHIRMAMEG SRAIKDNAKE FVPHPDNTKA TTPEGVARYK AYIERAVWYG ASANTVDGML GQIFARDPV FTGPEDKFDM LINDVDGSGL SIHQQARDSA EDALSLGRGG LFVDYSYVTT NGVSEAQEES GEARPYIKFI A AEDILNWR ...String:
MRDSNNIKYV REDAKKMHKL WAHIRMAMEG SRAIKDNAKE FVPHPDNTKA TTPEGVARYK AYIERAVWYG ASANTVDGML GQIFARDPV FTGPEDKFDM LINDVDGSGL SIHQQARDSA EDALSLGRGG LFVDYSYVTT NGVSEAQEES GEARPYIKFI A AEDILNWR ERWVNGAKRT TLLVFREESD ADDDGYQIYK EEVWRELRLV DGTYWQRTWR ENDGQLYVDD WISPTKADGS QF DEIPFVI FGSKNNDPTI DMPPMRDLVE LNIAHFRNSA DYEEACFICG QPTLFLSGLT EHWVKNVLGG AVVIGSRDAV PLP VNAKPE LLQAEGNGMV KEAMDQKERQ MVALGAKLID SDKTQRTFGE ASMEAAAQNS VLSRVSKNVS DAYTKALRWA AMFL GLDEK IEYELNSDFD INKMSPEELA AVISAWQSNA ISFTEMRWQI KKGGRAYLED EDMRNESEQD DPLKLDITKP DPNED PNAS EDDQTDPNDE TKEKDAETGG AE

UniProtKB: Portal 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

Startup modelType of model: OTHER / Details: De novo SGD model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36368
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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