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- EMDB-33584: CryoEM structure of Klebsiella phage Kp9 icosahedral head -

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Basic information

Entry
Database: EMDB / ID: EMD-33584
TitleCryoEM structure of Klebsiella phage Kp9 icosahedral head
Map data
Sample
  • Virus: Klebsiella phage Kp9 (virus)
    • Protein or peptide: phage capsid protein
KeywordsPodophage / icosahedral head / VIRUS
Biological speciesKlebsiella phage Kp9 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuang L / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers
Authors: Huang L / Xiang Y
History
DepositionJun 9, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33584.png

Downloads & links

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Map

FileDownload / File: emd_33584.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.)
1.07 Å/pix.
x 1000 pix.
= 1074.2 Å		1.07 Å/pix.
x 1000 pix.
= 1074.2 Å		1.07 Å/pix.
x 1000 pix.
= 1074.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.043986667 - 0.08256672
Average (Standard dev.)0.0004190359 (±0.0026976466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1074.2001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33584_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_33584_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 : Klebsiella phage Kp9

EntireName: Klebsiella phage Kp9 (virus)
Components
  • Virus: Klebsiella phage Kp9 (virus)
    • Protein or peptide: phage capsid protein

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Supramolecule #1: Klebsiella phage Kp9

SupramoleculeName: Klebsiella phage Kp9 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936516 / Sci species name: Klebsiella phage Kp9 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Klebsiella pneumoniae ATCC 43816 (bacteria)
Virus shellShell ID: 1 / Diameter: 600.0 Å / T number (triangulation number): 7

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Macromolecule #1: phage capsid protein

MacromoleculeName: phage capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage Kp9 (virus)
Molecular weightTheoretical: 36.648387 KDa
SequenceString: MANMQGGQRL GTNQGKGQSA ADKLALFLKV FGGEVLTAFA RTSVTTNRHM QRQISSGKSA QFPVIGRTKA AYLQPGESLD DKRKDIKHT EKTINIDGLL TADVLIYDIE DAMNHYDVRS EYTSQIGESL AMAADGAVLA ELAGLVNLAD SVNENIAGLG K PSLLEVGL ...String:
MANMQGGQRL GTNQGKGQSA ADKLALFLKV FGGEVLTAFA RTSVTTNRHM QRQISSGKSA QFPVIGRTKA AYLQPGESLD DKRKDIKHT EKTINIDGLL TADVLIYDIE DAMNHYDVRS EYTSQIGESL AMAADGAVLA ELAGLVNLAD SVNENIAGLG K PSLLEVGL KADLTDPVKL GQAVIAQLTI ARAALTKNYV PANDRTFYTT PDVYSAILAA LMPNAANYAA LIDPERGSIR NV MGFEVVE VPHLTAGGAG DDRPDEGAEA TNQKHAFPAA GGKVNKENVV GLFQHRSAVG TVKLKDLALE RARRTEYQAD QIV AKYAMG HGGLRPESAG ALVFTAASA

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 40835
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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