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- PDB-9ev2: Tail tube and extended tail sheath tube of Klebsiella phage KP1 v... -

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Basic information

Entry
Database: PDB / ID: 9ev2
TitleTail tube and extended tail sheath tube of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Components
  • Tail sheath protein
  • Tail tube protein
KeywordsVIRUS / Viral tail / sheath
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsOrlova, E.V. / Isupov, M.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Authors: Orlova, E.V. / Isupov, M.N.
History
DepositionMar 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S1: Tail sheath protein
S2: Tail sheath protein
SA: Tail sheath protein
SB: Tail sheath protein
SC: Tail sheath protein
SD: Tail sheath protein
SE: Tail sheath protein
SF: Tail sheath protein
SG: Tail sheath protein
SH: Tail sheath protein
SI: Tail sheath protein
SJ: Tail sheath protein
SK: Tail sheath protein
SL: Tail sheath protein
SM: Tail sheath protein
SN: Tail sheath protein
SO: Tail sheath protein
SP: Tail sheath protein
SQ: Tail sheath protein
SR: Tail sheath protein
SS: Tail sheath protein
ST: Tail sheath protein
SU: Tail sheath protein
SV: Tail sheath protein
SW: Tail sheath protein
SX: Tail sheath protein
SY: Tail sheath protein
SZ: Tail sheath protein
Sa: Tail sheath protein
Sb: Tail sheath protein
Sc: Tail sheath protein
Sd: Tail sheath protein
Se: Tail sheath protein
Sf: Tail sheath protein
Sg: Tail sheath protein
Sh: Tail sheath protein
Si: Tail sheath protein
Sj: Tail sheath protein
Sk: Tail sheath protein
Sl: Tail sheath protein
Sm: Tail sheath protein
Sn: Tail sheath protein
So: Tail sheath protein
Sp: Tail sheath protein
Sq: Tail sheath protein
Sr: Tail sheath protein
Ss: Tail sheath protein
St: Tail sheath protein
Su: Tail sheath protein
Sv: Tail sheath protein
Sw: Tail sheath protein
Sx: Tail sheath protein
Sy: Tail sheath protein
Sz: Tail sheath protein
T1: Tail tube protein
T2: Tail tube protein
TA: Tail tube protein
TB: Tail tube protein
TC: Tail tube protein
TD: Tail tube protein
TE: Tail tube protein
TF: Tail tube protein
TG: Tail tube protein
TH: Tail tube protein
TI: Tail tube protein
TJ: Tail tube protein
TK: Tail tube protein
TL: Tail tube protein
TM: Tail tube protein
TN: Tail tube protein
TO: Tail tube protein
TP: Tail tube protein
TQ: Tail tube protein
TR: Tail tube protein
TS: Tail tube protein
TT: Tail tube protein
TU: Tail tube protein
TV: Tail tube protein
TW: Tail tube protein
TX: Tail tube protein
TY: Tail tube protein
TZ: Tail tube protein
Ta: Tail tube protein
Tb: Tail tube protein
Tc: Tail tube protein
Td: Tail tube protein
Te: Tail tube protein
Tf: Tail tube protein
Tg: Tail tube protein
Th: Tail tube protein
Ti: Tail tube protein
Tj: Tail tube protein
Tk: Tail tube protein
Tl: Tail tube protein
Tm: Tail tube protein
Tn: Tail tube protein
To: Tail tube protein
Tp: Tail tube protein
Tq: Tail tube protein
Tr: Tail tube protein
Ts: Tail tube protein
Tt: Tail tube protein
Tu: Tail tube protein
Tv: Tail tube protein
Tw: Tail tube protein
Tx: Tail tube protein
Ty: Tail tube protein
Tz: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)4,877,757108
Polymers4,877,757108
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Tail sheath protein


Mass: 71695.094 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5S7
#2: Protein ...
Tail tube protein


Mass: 18633.738 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5T6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Klebsiella phage KP1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Klebsiella phage KP1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Klebsiella phage KP1 variant vB_Kpn_Lilla1
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 92 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: Alignment 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 ...Details: Alignment 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
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 83505 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: OTHER
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93.6 K / Temperature (min): 78.7 K / Residual tilt: 68 mradians
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU2.4image acquisition
3cryoSPARC4.3image acquisition
5cryoSPARC4.3CTF correction
8MOLREPmodel fitting
9Cootmodel fitting
11cryoSPARC4.3initial Euler assignment
12cryoSPARC4.3final Euler assignment
13cryoSPARC4.3classification
14cryoSPARC4.33D reconstruction
15REFMACmodel refinement
16ISOLDEmodel refinement
17UCSF ChimeraXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 16.93 ° / Axial rise/subunit: 40.22 Å / Axial symmetry: C6
Particle selectionNum. of particles selected: 40161
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7017 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT

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