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- EMDB-19992: Tail tube and extended tail sheath tube of Klebsiella phage KP1 v... -

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Basic information

Entry
Database: EMDB / ID: EMD-19992
TitleTail tube and extended tail sheath tube of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Map data
Sample
  • Virus: Klebsiella phage KP1 (virus)
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tube protein
KeywordsViral tail / sheath / VIRUS
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / structural molecule activity
Similarity search - Function
: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain ...: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Tail sheath protein / Tail tube protein
Similarity search - Component
Biological speciesKlebsiella phage KP1 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsOrlova EV / Isupov MN
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Authors: Orlova EV / Isupov MN
History
DepositionMar 28, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19992.png

Downloads & links

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Map

FileDownload / File: emd_19992.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.34
Minimum - Maximum-0.4021123 - 0.86827135
Average (Standard dev.)0.008655765 (±0.05176212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19992_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_19992_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 KP1

EntireName: Klebsiella phage KP1 (virus)
Components
  • Virus: Klebsiella phage KP1 (virus)
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tube protein

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Supramolecule #1: Klebsiella phage KP1

SupramoleculeName: Klebsiella phage KP1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2070202 / Sci species name: Klebsiella phage KP1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 54 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 71.695094 KDa
SequenceString: MPLVSPGIEL KETSVQSTVV LNATGRAAIV GKFQWGPAYQ VTQITNEVEL VDMFGGPNNQ TADYFMSAMN FLQYGNDLRT VRVVNREAA KNASPLVDNI EWEITTAGSN YEVGDKITVK YADQVVDDTG SVTEVDSDGK IKSVFIPTSK IIAYAKSINQ Y PDLGSSWT ...String:
MPLVSPGIEL KETSVQSTVV LNATGRAAIV GKFQWGPAYQ VTQITNEVEL VDMFGGPNNQ TADYFMSAMN FLQYGNDLRT VRVVNREAA KNASPLVDNI EWEITTAGSN YEVGDKITVK YADQVVDDTG SVTEVDSDGK IKSVFIPTSK IIAYAKSINQ Y PDLGSSWT TTITSQSSGV SAVITLGKII SDSTVLLTEP ETAHEEMTKT EFQTALAKYK MPGIVAAYPG ELGNQLEIEI VS KAAFDKG EQLTIYPAGG KRASTAKAVF GYGPQTDTQY AIIVRRDGAV VESAVLSTSR QDKDIYGNNI FMDDYFSKGS SRY IFATAQ GWPEGFAGVI RLGGGVSANE SVTAGDLIQG WDLFGDREAL RVNLLIAGAC AGETDEIAST VQKHVSSIAD ERQD CLALI SPPRSTIVNI PLTRAVDNLI DWRQGEGSYD SANMNINTTY AAIDGNYKYQ YDKYNDVNRW VPLAADIAGL CARTD DIAQ PWMSPAGYRR GQILNCIKLA IEPRQAHRDR MYQAGINPVT GQGTGDGFIL FGDKTATTVP TPFDRINVRR LFNMLK NNI GDSSKWQLFE LNDNFTRSSF RMETSQYLAG IKALGGVYDF RVVCDTTNNT PAVIDRNEFV ASFYIKPARS INYITLN FV ATATGADFDE LIGP

UniProtKB: Tail sheath protein

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Macromolecule #2: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 54 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage KP1 (virus)
Molecular weightTheoretical: 18.633738 KDa
SequenceString:
MELTDITRAF ESGDFARPNL FEVEIPYLGR NFSFKCKAAP MPAGIVEKVP VGYMNRKINV AGDRTYDDWT VTIYNDDKHE VRKAIIAWQ AQAHAQGNDI SGMTPADYKK VATVRQFSRD GKTITNEHTI TGLWPTNVGE VQMDWDSNNE VETFETTFAI D WWE

UniProtKB: Tail tube protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 92.0 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsKlebsiella phage KP1 variant vB_Kpn_Lilla1

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 78.7 K / Max: 93.6 K
DetailsAlignment procedure: EPU Autocoma and Autosrigmate Residual tilt (if alignment procedure is coma free, mrad): 68 Software used to collect images EPU 2.4, Tomo 5.13 Film/CCD/Direct electron detector model*: post GIF K3
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 83505 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 40.22 Å
Applied symmetry - Helical parameters - Δ&Phi: 16.93 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 7017
Segment selectionNumber selected: 40161 / Software - Name: cryoSPARC
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9ev2:
Tail tube and extended tail sheath tube of Klebsiella phage KP1 variant vB_Kpn_Lilla1

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