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- PDB-9sz9: Capsid structure of Lactococcus phage Nocturne116 -

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Basic information

Entry
Database: PDB / ID: 9sz9
TitleCapsid structure of Lactococcus phage Nocturne116
Components
  • Capsid vertex protein
  • Major capsid protein
KeywordsVIRUS / Bacteriophage / capsid / HK97 fold
Biological speciesLactococcus phage Nocturne116 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.63 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

Downloads & links

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Assembly

Deposited unit
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
Aa: Major capsid protein
Ab: Major capsid protein
Ac: Major capsid protein
Ad: Major capsid protein
Ae: Major capsid protein
Af: Major capsid protein
Ag: Major capsid protein
Ah: Major capsid protein
Ai: Major capsid protein
Aj: Major capsid protein
Ak: Major capsid protein
Al: Major capsid protein
Am: Major capsid protein
An: Major capsid protein
Ao: Major capsid protein
Ap: Major capsid protein
Aq: Major capsid protein
Ar: Major capsid protein
As: Major capsid protein
At: Major capsid protein
Au: Major capsid protein
Av: Major capsid protein
Aw: Major capsid protein
Ax: Major capsid protein
Ay: Major capsid protein
Az: Major capsid protein
A0: Major capsid protein
A1: Major capsid protein
A2: Major capsid protein
A3: Major capsid protein
A4: Major capsid protein
A5: Major capsid protein
A6: Major capsid protein
A7: Major capsid protein
FA: Capsid vertex protein
FB: Capsid vertex protein
FC: Capsid vertex protein
FD: Capsid vertex protein
FE: Capsid vertex protein
FF: Capsid vertex protein
FG: Capsid vertex protein
FH: Capsid vertex protein
FI: Capsid vertex protein
FJ: Capsid vertex protein
FK: Capsid vertex protein


Theoretical massNumber of molelcules
Total (without water)3,712,86671
Polymers3,712,86671
Non-polymers00
Water00
1
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
Aa: Major capsid protein
Ab: Major capsid protein
Ac: Major capsid protein
Ad: Major capsid protein
Ae: Major capsid protein
Af: Major capsid protein
Ag: Major capsid protein
Ah: Major capsid protein
Ai: Major capsid protein
Aj: Major capsid protein
Ak: Major capsid protein
Al: Major capsid protein
Am: Major capsid protein
An: Major capsid protein
Ao: Major capsid protein
Ap: Major capsid protein
Aq: Major capsid protein
Ar: Major capsid protein
As: Major capsid protein
At: Major capsid protein
Au: Major capsid protein
Av: Major capsid protein
Aw: Major capsid protein
Ax: Major capsid protein
Ay: Major capsid protein
Az: Major capsid protein
A0: Major capsid protein
A1: Major capsid protein
A2: Major capsid protein
A3: Major capsid protein
A4: Major capsid protein
A5: Major capsid protein
A6: Major capsid protein
A7: Major capsid protein
FA: Capsid vertex protein
FB: Capsid vertex protein
FC: Capsid vertex protein
FD: Capsid vertex protein
FE: Capsid vertex protein
FF: Capsid vertex protein
FG: Capsid vertex protein
FH: Capsid vertex protein
FI: Capsid vertex protein
FJ: Capsid vertex protein
FK: Capsid vertex protein
x 5


Theoretical massNumber of molelcules
Total (without water)18,564,332355
Polymers18,564,332355
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

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Components

#1: Protein ...
Major capsid protein


Mass: 57442.773 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage Nocturne116 (virus)
#2: Protein
Capsid vertex protein


Mass: 24209.094 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage Nocturne116 (virus)
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1Lactococcus phage Nocturne116VIRUSall0NATURAL
2CapsidCOMPLEXall1NATURALProlate capsid composed of major head protein and vertex 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
IDNameVersionCategory
1RELION4.0.1particle selection
2PHENIX1.21.2_5419model refinement
5CTFFIND4.1.14CTF correction
10RELION4.0.1initial Euler assignment
11RELION4.0.1final Euler assignment
13RELION5.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29793 / Symmetry type: POINT
Atomic model buildingDetails: Model produced using ModelAngelo / Source name: Other / Type: experimental model

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