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- EMDB-45163: Bacteriophage Sf14 Capsid Empty Icosahedral reconstruction -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45163
TitleBacteriophage Sf14 Capsid Empty Icosahedral reconstruction
Map data
Sample
  • Virus: Shigella phage Sf14 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Putative structural protein
    • Protein or peptide: Putative tail protein
KeywordsSf14 / VIRUS
Function / homology
Function and homology information


host cell cytoplasm
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 ...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
Putative tail protein / Major capsid protein / Putative structural protein
Similarity search - Component
Biological speciesShigella phage Sf14 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSubramanian S / Kerns HR / Braverman SG / Doore SM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI170608 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116789 United States
CitationJournal: To Be Published
Title: Structure of the Shigella flexneri bacteriophage Sf14 - empty capsid
Authors: Subramanian S / Kerns HR / Braverman SG / Doore SM
History
DepositionMay 31, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45163.png

Downloads & links

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Map

FileDownload / File: emd_45163.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 1000 pix.
= 1224. Å		1.22 Å/pix.
x 1000 pix.
= 1224. Å		1.22 Å/pix.
x 1000 pix.
= 1224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.224 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.651
Minimum - Maximum-2.864013 - 5.9227223
Average (Standard dev.)0.00069008296 (±0.24873541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-499-499-499
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45163_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45163_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_45163_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 : Shigella phage Sf14

EntireName: Shigella phage Sf14 (virus)
Components
  • Virus: Shigella phage Sf14 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Putative structural protein
    • Protein or peptide: Putative tail protein

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Supramolecule #1: Shigella phage Sf14

SupramoleculeName: Shigella phage Sf14 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2024304 / Sci species name: Shigella phage Sf14 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Shigella flexneri Y (bacteria)

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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: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 41.595992 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MLTNSEKSRF FLADLTGEVQ SIPNTYGYIS GLGLFRSAPQ TQTTFLMDLT DWDISLLDAV DRTSRKAETS APERVRQISF PMMYFKEVE SITPDEIQGV RQPGTANELT TEAVVRAKKL MKIRTKFDIT REFLFMQALK GKVIDANGVL YADLYKQFDV T KKTIYFDL ...String:
MLTNSEKSRF FLADLTGEVQ SIPNTYGYIS GLGLFRSAPQ TQTTFLMDLT DWDISLLDAV DRTSRKAETS APERVRQISF PMMYFKEVE SITPDEIQGV RQPGTANELT TEAVVRAKKL MKIRTKFDIT REFLFMQALK GKVIDANGVL YADLYKQFDV T KKTIYFDL DNPNSDIDAH IEDLRMHMED EAKTGTVING EEIHIVVDRT FFSKLIKHPK IRDAYLAQQT PLAWQQITGS LR TGGTDGV QAHMNRFYYG GVVFVQYNGK FKDKRGKTHT LVSIDGVSDT NVGVGHAFPN VAMLGEANNI FEVAYAPCPK MGY ANTLGQ ELYVFEYEKD RDEGIDFEAH SYMLPYCTRP QLLVDVRSDA E

UniProtKB: Major capsid protein

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Macromolecule #2: Putative structural protein

MacromoleculeName: Putative structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 13.574381 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString:
MAYQGFTKLG EREPLNDIIL WEEITPTGHS RKEYAPVAST EYRVGEVLKA DGSKVAAGQE AQADSVCIVN FYADLQLSYH GQLKVVGIY RDAELKDLLK LESGVDAAAV KSALKAKGID FVPTGL

UniProtKB: Putative structural protein

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Macromolecule #3: Putative tail protein

MacromoleculeName: Putative tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Sf14 (virus)
Molecular weightTheoretical: 39.336539 KDa
Recombinant expressionOrganism: Shigella flexneri Y (bacteria)
SequenceString: MIKAKTYPDF KEFVKDFVAN VKAGKRYDFR KYQEAVLPLT YSSPWPESDI PEVTDFNYTP DYTVPFSEEL LYSVGAQMRT ADFFMDLQY AIINGKDVDT VYCEWLARVK PFSMLNAKLK DSAQPPVITT QPTGGAVNEG SAINLSIVAT NATSYQWKKG S SDISGATS ...String:
MIKAKTYPDF KEFVKDFVAN VKAGKRYDFR KYQEAVLPLT YSSPWPESDI PEVTDFNYTP DYTVPFSEEL LYSVGAQMRT ADFFMDLQY AIINGKDVDT VYCEWLARVK PFSMLNAKLK DSAQPPVITT QPTGGAVNEG SAINLSIVAT NATSYQWKKG S SDISGATS ATYTKAGAVP ADAGSYTCVV TNDVGSTTSD AAVITINPLP VITTQPTSKA VNESSTLTLS VVATGATSYQ WK KNGTNIS GATSATYSKA NAKTTDAGSY TCVVTNAVGS VTSNAATVTI NPLPVITVQP QDQDLTVGQT LTISITATGA TGY QWRKGN SNISGATSAT YTKASVTTAD DGNYDCVVTN AVGSVTSHQA KVQVTA

UniProtKB: Putative tail 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
Component:
ConcentrationFormulaName
10.0 mMTristris(hydroxymethyl)aminomethane
10.0 mMMgCl2magnesium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Full capsid was used as the initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98511
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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