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- EMDB-28226: Bacteriophage HRP29 Icosohedral Reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-28226
TitleBacteriophage HRP29 Icosohedral Reconstruction
Map data
SampleShigella phage HRP29 != Shigella phage Buco

Shigella phage HRP29

  • Virus: Shigella phage Buco (virus)
    • Protein or peptide: Gp37
    • Protein or peptide: Gp47
    • Protein or peptide: Gp48
KeywordsHRP29 / VIRUS
Function / homologyUncharacterized protein / Putative capsid protein / Uncharacterized protein
Function and homology information
Biological speciesShigella phage Buco (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSubramanian S / Bergland Drarvik SM / Parent KN
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110185 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140803 United States
National Science Foundation (NSF, United States)1750125 United States
CitationJournal: To Be Published
Title: Structure of Shigella bacteriophage HRP29
Authors: Subramanian S / Bergland Drarvik SM / Parent KN
History
DepositionSep 23, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28226.png

Downloads & links

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Map

FileDownload / File: emd_28226.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 800 pix.
= 1305.6 Å		1.63 Å/pix.
x 800 pix.
= 1305.6 Å		1.63 Å/pix.
x 800 pix.
= 1305.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.059508312 - 0.14039189
Average (Standard dev.)0.000497992 (±0.0039269654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 1305.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28226_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28226_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_28226_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 HRP29

EntireName: Shigella phage HRP29
Components
  • Virus: Shigella phage Buco (virus)
    • Protein or peptide: Gp37
    • Protein or peptide: Gp47
    • Protein or peptide: Gp48

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Supramolecule #1: Shigella phage Buco

SupramoleculeName: Shigella phage Buco / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2530183 / Sci species name: Shigella phage Buco / 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: Gp37

MacromoleculeName: Gp37 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 36.911305 KDa
SequenceString: MANTDYAGNL TRPHWGGAAS DVDIHLEVYQ NEVDTRFQYQ AMFLGLSSQR SVADRSNTYR IDRLNTSSVK GRTSGVALEP TPVRNDKML IVVDTVLYIR NPIDYQDDWT APDFLTEMGQ NNGSEFAEVF DQAHLIQLIK GRSWVAPAHL KPAFSDGIEI E ATIDSDVT ...String:
MANTDYAGNL TRPHWGGAAS DVDIHLEVYQ NEVDTRFQYQ AMFLGLSSQR SVADRSNTYR IDRLNTSSVK GRTSGVALEP TPVRNDKML IVVDTVLYIR NPIDYQDDWT APDFLTEMGQ NNGSEFAEVF DQAHLIQLIK GRSWVAPAHL KPAFSDGIEI E ATIDSDVT TQAGMEANAI AINQAHKAGI DELIKRKVPL NDMITLVSTE IYSLLLEHPK LFNKDWGDAN ANGYKERRAV LM NGIPVVE CTEFPDAGTH PLGSAYTVTA DDAKCRMVTF SKSRTLVTVE AKPFTSRIWD DEQNFANVLD CYAMYQVGER RPD TAAVVK FNEAP

UniProtKB: Putative capsid protein

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Macromolecule #2: Gp47

MacromoleculeName: Gp47 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 13.021738 KDa
SequenceString:
MASIIAAKAK DKQYEIVGKA QNLLKQVQPL YNVGFSTTAL DLLNAYFTYM QAQGFATTRA GTGFVSDGAK LARLDNMLDQ VSKTGYVVL TGTGAPIGET SGTAFDTSFT ALRAAFLAAT TPTTA

UniProtKB: Uncharacterized protein

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Macromolecule #3: Gp48

MacromoleculeName: Gp48 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage Buco (virus)
Molecular weightTheoretical: 6.424381 KDa
SequenceString:
MAVAKATAAQ RQEFLRQLNI LAKDMYQALT QPQDLAYRGP EIDAKIAALE AATAAVKAAS

UniProtKB: Uncharacterized 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:
ConcentrationNameFormula
10.0 mMtris(hydroxymethyl)aminomethane
10.0 mMmagnesium chlorideMgCl2
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: EMDB MAP
EMDB ID:

5730

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 38666
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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