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- EMDB-38212: Portal-vertex of SH-Ab15497 in C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-38212
TitlePortal-vertex of SH-Ab15497 in C1 symmetry
Map data
Sample
  • Virus: Acinetobacter phage SH-Ab 15497 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Major capsid protein
Keywordssymmetry-mismatch / VIRAL PROTEIN
Function / homologyDomain of unknown function DUF4055 / Domain of unknown function (DUF4055) / Major capsid protein 13-like / Major capsid protein 13-like / Portal protein / Major capsid protein
Function and homology information
Biological speciesAcinetobacter phage SH-Ab 15497 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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: Portal-vertex of SH-Ab15497 in C1 symmetry
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_38212.png

Downloads & links

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Map

FileDownload / File: emd_38212.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: 0.008
Minimum - Maximum-0.012861515 - 0.028904105
Average (Standard dev.)-0.000010946125 (±0.002978493)
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: #2

Fileemd_38212_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38212_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
    • 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
Host (natural)Organism: Acinetobacter baumannii (bacteria)
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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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 10 / 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

Startup modelType of model: OTHER / Details: De novo SGD model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 72915
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 14873 / 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-8xb6:
Portal-vertex of SH-Ab15497 in C1 symmetry

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