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- PDB-9f4b: Pre-assembled baseplate cup of Klebsiella phage KP1 variant vB_Kp... -

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Basic information

Entry
Database: PDB / ID: 9f4b
TitlePre-assembled baseplate cup of Klebsiella phage KP1 variant vB_Kpn_Lilla1
Components
  • (Baseplate wedge ...) x 7
  • Baseplate central spike protein
  • Baseplate hub subunit tail length determinator
  • Baseplate subunit
  • Baseplate tail tube cap
  • Gp12 short tail fibers
  • IraD/Gp25-like domain-containing protein
  • Phospholipase
  • Putative baseplate hub subunit
  • Tail tube protein
KeywordsVIRUS / Baseplate cup / baseplate wedge / fibers
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / viral tail assembly / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / symbiont entry into host cell via disruption of host cell envelope / viral tail assembly / viral release from host cell / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / structural molecule activity / membrane
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain ...Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Baseplate wedge protein gp53, bacteriophage T4 / Baseplate wedge protein gp7 / : / : / : / Base plate wedge protein 53 / Baseplate wedge protein gp7, domain V / Baseplate wedge protein gp7, helical domain / Baseplate wedge protein gp7, domain VI / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate wedge protein gp10 / Baseplate wedge protein gp6 / : / : / : / : / : / : / Baseplate wedge protein gp6-like, helical domain / Baseplate structural protein gp6, C-terminal domain I / Baseplate structural protein gp6, C-terminal domain II / Baseplate wedge protein gp6, domain II / Baseplate structural protein gp6, C-terminal domain III / Baseplate wedge protein gp10 domain 3 / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / : / Baseplate structural protein Gp10, C-terminal domain / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / : / Bacteriophage T4 gp9/10-like protein, N-terminal / Bacteriophage T4 gp9/10-like protein, C-terminal / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Bacteriophage T4 gp5 C-terminal trimerisation domain / PAAR motif / PAAR motif / IraD/Gp25-like / Baseplate wedge protein gp25 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Lysozyme-like domain superfamily / Peptidase S1, PA clan, chymotrypsin-like fold
Similarity search - Domain/homology
: / IraD/Gp25-like domain-containing protein / Baseplate wedge protein gp6 / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Baseplate wedge protein gp10 / Baseplate wedge subunit and tail pin / Tail tube protein / Baseplate wedge protein gp7 / Phospholipase ...: / IraD/Gp25-like domain-containing protein / Baseplate wedge protein gp6 / Baseplate wedge subunit / Baseplate wedge tail fiber connector / Baseplate wedge protein gp10 / Baseplate wedge subunit and tail pin / Tail tube protein / Baseplate wedge protein gp7 / Phospholipase / Baseplate hub subunit tail length determinator / Baseplate tail tube cap / Baseplate wedge subunit / Baseplate subunit / Gp12 short tail fibers / Putative baseplate hub subunit / Baseplate central spike protein
Similarity search - Component
Biological speciesKlebsiella phage KP1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 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
DepositionApr 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 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
AT: Baseplate wedge protein gp6
AV: Baseplate wedge protein gp6
AX: Baseplate wedge protein gp6
AS: Baseplate wedge protein gp6
AU: Baseplate wedge protein gp6
AW: Baseplate wedge protein gp6
AN: Baseplate wedge protein gp6
AP: Baseplate wedge protein gp6
AR: Baseplate wedge protein gp6
AM: Baseplate wedge protein gp6
AO: Baseplate wedge protein gp6
AQ: Baseplate wedge protein gp6
BL: Baseplate tail tube cap
BN: Baseplate tail tube cap
BP: Baseplate tail tube cap
BK: Baseplate tail tube cap
BM: Baseplate tail tube cap
BO: Baseplate tail tube cap
BQ: Baseplate subunit
BR: Baseplate subunit
BS: Baseplate subunit
BT: Baseplate subunit
BU: Baseplate subunit
BV: Baseplate subunit
AH: Baseplate wedge subunit
AJ: Baseplate wedge subunit
AL: Baseplate wedge subunit
AG: Baseplate wedge subunit
AI: Baseplate wedge subunit
AK: Baseplate wedge subunit
BB: Baseplate central spike protein
BC: Baseplate central spike protein
BD: Baseplate central spike protein
BA: Phospholipase
AY: Baseplate wedge protein gp7
A2: Baseplate wedge protein gp7
AZ: Baseplate wedge protein gp7
A0: Baseplate wedge protein gp7
A1: Baseplate wedge protein gp7
A3: Baseplate wedge protein gp7
Ad: Baseplate wedge subunit
Ac: Baseplate wedge subunit
Ab: Baseplate wedge subunit
Aa: Baseplate wedge subunit
Ae: Baseplate wedge subunit
Af: Baseplate wedge subunit
A4: Baseplate wedge subunit
A5: Baseplate wedge subunit
A6: Baseplate wedge subunit
A7: Baseplate wedge subunit
A8: Baseplate wedge subunit
A9: Baseplate wedge subunit
LA: Baseplate wedge tail fiber connector
LB: Baseplate wedge tail fiber connector
LC: Baseplate wedge tail fiber connector
LD: Baseplate wedge tail fiber connector
LE: Baseplate wedge tail fiber connector
LF: Baseplate wedge tail fiber connector
LG: Baseplate wedge tail fiber connector
LH: Baseplate wedge tail fiber connector
LI: Baseplate wedge tail fiber connector
LJ: Baseplate wedge tail fiber connector
LK: Baseplate wedge tail fiber connector
LL: Baseplate wedge tail fiber connector
LM: Baseplate wedge tail fiber connector
LN: Baseplate wedge tail fiber connector
LO: Baseplate wedge tail fiber connector
LP: Baseplate wedge tail fiber connector
LQ: Baseplate wedge tail fiber connector
LR: Baseplate wedge tail fiber connector
FA: Baseplate wedge protein gp10
FB: Baseplate wedge protein gp10
FC: Baseplate wedge protein gp10
FJ: Baseplate wedge protein gp10
FK: Baseplate wedge protein gp10
FL: Baseplate wedge protein gp10
FS: Baseplate wedge protein gp10
FT: Baseplate wedge protein gp10
FU: Baseplate wedge protein gp10
Fb: Baseplate wedge protein gp10
Fc: Baseplate wedge protein gp10
Fd: Baseplate wedge protein gp10
Fk: Baseplate wedge protein gp10
Fl: Baseplate wedge protein gp10
Fm: Baseplate wedge protein gp10
Ft: Baseplate wedge protein gp10
Fu: Baseplate wedge protein gp10
Fv: Baseplate wedge protein gp10
FD: Baseplate wedge subunit and tail pin
FE: Baseplate wedge subunit and tail pin
FF: Baseplate wedge subunit and tail pin
FM: Baseplate wedge subunit and tail pin
FN: Baseplate wedge subunit and tail pin
FO: Baseplate wedge subunit and tail pin
FV: Baseplate wedge subunit and tail pin
FW: Baseplate wedge subunit and tail pin
FX: Baseplate wedge subunit and tail pin
Fe: Baseplate wedge subunit and tail pin
Ff: Baseplate wedge subunit and tail pin
Fg: Baseplate wedge subunit and tail pin
Fn: Baseplate wedge subunit and tail pin
Fo: Baseplate wedge subunit and tail pin
Fp: Baseplate wedge subunit and tail pin
Fw: Baseplate wedge subunit and tail pin
Fx: Baseplate wedge subunit and tail pin
Fy: Baseplate wedge subunit and tail pin
FG: Gp12 short tail fibers
FI: Gp12 short tail fibers
FH: Gp12 short tail fibers
FP: Gp12 short tail fibers
FR: Gp12 short tail fibers
FQ: Gp12 short tail fibers
FY: Gp12 short tail fibers
Fa: Gp12 short tail fibers
FZ: Gp12 short tail fibers
Fh: Gp12 short tail fibers
Fj: Gp12 short tail fibers
Fi: Gp12 short tail fibers
Fq: Gp12 short tail fibers
Fs: Gp12 short tail fibers
Fr: Gp12 short tail fibers
Fz: Gp12 short tail fibers
F2: Gp12 short tail fibers
F1: Gp12 short tail fibers
BW: Tail tube protein
BX: Tail tube protein
BY: Tail tube protein
BZ: Tail tube protein
B1: Tail tube protein
B2: Tail tube protein
B3: Tail tube protein
B4: Tail tube protein
B5: Tail tube protein
B6: Tail tube protein
B7: Tail tube protein
B8: Tail tube protein
AA: IraD/Gp25-like domain-containing protein
AB: IraD/Gp25-like domain-containing protein
AC: IraD/Gp25-like domain-containing protein
AD: IraD/Gp25-like domain-containing protein
AE: IraD/Gp25-like domain-containing protein
AF: IraD/Gp25-like domain-containing protein
BE: Putative baseplate hub subunit
BF: Putative baseplate hub subunit
BG: Putative baseplate hub subunit
BH: Baseplate hub subunit tail length determinator
BI: Baseplate hub subunit tail length determinator
BJ: Baseplate hub subunit tail length determinator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,577,152161
Polymers6,576,490148
Non-polymers66213
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

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Baseplate wedge ... , 7 types, 90 molecules ATAVAXASAUAWANAPARAMAOAQAHAJALAGAIAKAYA2AZA0A1A3AdAcAbAaAeAf...

#1: Protein
Baseplate wedge protein gp6


Mass: 73689.242 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5R4
#4: Protein
Baseplate wedge subunit


Mass: 24693.420 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5R5
#7: Protein
Baseplate wedge protein gp7


Mass: 119645.719 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5T9
#8: Protein
Baseplate wedge subunit


Mass: 38704.387 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2Z4QAY9
#9: Protein
Baseplate wedge tail fiber connector


Mass: 32380.195 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5S1
#10: Protein
Baseplate wedge protein gp10


Mass: 66712.070 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5S8
#11: Protein
Baseplate wedge subunit and tail pin


Mass: 24534.469 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5T5

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Protein , 9 types, 58 molecules BLBNBPBKBMBOBQBRBSBTBUBVBBBCBDBAFGFIFHFPFRFQFYFaFZFhFjFiFqFs...

#2: Protein
Baseplate tail tube cap


Mass: 38263.664 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V618
#3: Protein
Baseplate subunit


Mass: 33716.129 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A7I8V4E3
#5: Protein Baseplate central spike protein / Peptidoglycan hydrolase


Mass: 63317.457 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A976LXP5, lysozyme
#6: Protein Phospholipase


Mass: 10096.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5W6
#12: Protein
Gp12 short tail fibers


Mass: 48092.477 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A7R8MRX7
#13: Protein
Tail tube protein


Mass: 18633.738 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5T6
#14: Protein
IraD/Gp25-like domain-containing protein


Mass: 15382.360 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A0K1Y5J2
#15: Protein Putative baseplate hub subunit


Mass: 43526.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A7T3TJP2
#16: Protein Baseplate hub subunit tail length determinator


Mass: 64127.020 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage KP1 (virus) / References: UniProt: A0A2K9V5Z4

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Non-polymers , 3 types, 13 molecules

#17: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#18: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: vB_Kpn_Lilla1 / Type: VIRUS / Entity ID: #1-#16 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: vB_Kpn_Lilla1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Klebsiella
Buffer solutionpH: 7.5 / Details: 100mM NaCl, 8mM MgSO4, 50mM Tris-HCl
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 recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4
Image scansSampling size: 5 µm / Width: 4092 / Height: 5760

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
2EPU2.4image acquisition
3cryoSPARC4.3image acquisition
5cryoSPARC4.3CTF correction
8MOLREPmodel fitting
10cryoSPARC4.3initial Euler assignment
11cryoSPARC4.3final Euler assignment
12cryoSPARC4.3classification
13cryoSPARC4.33D reconstruction
14REFMACmodel refinement
15ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 34529
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34528 / Algorithm: FOURIER SPACE / Num. of class averages: 98 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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