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- PDB-9szd: Tail structure of Lactococcus phage Nocturne116 -

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Basic information

Entry
Database: PDB / ID: 9szd
TitleTail structure of Lactococcus phage Nocturne116
ComponentsMajor tail shaft protein
KeywordsVIRUS / Bacteriophage / tail
Function / homology:
Function and homology information
Biological speciesLactococcus phage Nocturne116 (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsRumnieks, J. / Tars, K.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Union (EU)5.2.1.1.i.0/2/24/I/CFLA/001European Union
iNEXT-Discovery24421European Union
CitationJournal: To Be Published
Title: Three-dimensional structure of Lactococcus bacteriophage Nocturne116
Authors: Rumnieks, J. / Tars, K.
History
DepositionOct 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major tail shaft protein


Theoretical massNumber of molelcules
Total (without water)23,7191
Polymers23,7191
Non-polymers00
Water00
1
A: Major tail shaft protein
x 18


Theoretical massNumber of molelcules
Total (without water)426,93618
Polymers426,93618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation17

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Components

#1: Protein Major tail shaft protein


Mass: 23718.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage Nocturne116 (virus) / References: UniProt: A0A8E5K7E1
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

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1Lactococcus phage Nocturne116VIRUSall0NATURAL
2Tail tubeCOMPLEXall1NATURALTail tube composed of stacked hexameric rings of the tail tube protein
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Lactococcus phage Nocturne116 (virus)2831179
32Lactococcus phage Nocturne116 (virus)2831179
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Lactococcus lactis / Strain: LNT
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl1
2100 mMsodium chlorideNaCl1
310 mMmagnesium sulfateMgSO41
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION4.0.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
7RELION5.0.0model fittingModelAngelo
9RELION4.0.1initial Euler assignment
10RELION4.0.1final Euler assignment
12RELION5.0.03D reconstruction
13Coot0.9.8model refinement
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 16.08 ° / Axial rise/subunit: 42.77 Å / Axial symmetry: C6
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249082 / Symmetry type: HELICAL
Atomic model buildingDetails: Model produced using ModelAngelo / Source name: Other / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00129268
ELECTRON MICROSCOPYf_angle_d0.35539708
ELECTRON MICROSCOPYf_dihedral_angle_d2.5794014
ELECTRON MICROSCOPYf_chiral_restr0.0424482
ELECTRON MICROSCOPYf_plane_restr0.0025130

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