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- PDB-9sza: Asymmetric structure of the capsid-portal complex of Lactococcus ... -

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Basic information

Entry
Database: PDB / ID: 9sza
TitleAsymmetric structure of the capsid-portal complex of Lactococcus phage Nocturne116
Components
  • DNA packaging protein
  • Major capsid protein
  • Putative portal protein
KeywordsVIRUS / Bacteriophage / capsid / portal
Function / homology: / : / :
Function and homology information
Biological speciesLactococcus phage Nocturne116 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 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
A: Putative portal protein
B: DNA packaging protein
C: Putative portal protein
D: DNA packaging protein
E: Putative portal protein
F: DNA packaging protein
G: Putative portal protein
H: DNA packaging protein
I: Putative portal protein
J: DNA packaging protein
K: Putative portal protein
L: DNA packaging protein
M: Putative portal protein
N: DNA packaging protein
O: Putative portal protein
P: DNA packaging protein
Q: Putative portal protein
R: DNA packaging protein
S: Putative portal protein
T: DNA packaging protein
U: Putative portal protein
V: DNA packaging protein
W: Putative portal protein
X: DNA packaging protein
a: Major capsid protein
b: Major capsid protein
c: Major capsid protein
d: Major capsid protein
e: Major capsid protein
f: Major capsid protein
g: Major capsid protein
h: Major capsid protein
i: Major capsid protein
j: Major capsid protein
k: Major capsid protein
l: Major capsid protein
m: Major capsid protein
n: Major capsid protein
o: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)1,409,36939
Polymers1,409,36939
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
Putative portal protein


Mass: 35015.707 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage Nocturne116 (virus) / References: UniProt: A0A8E5NQ91
#2: Protein
DNA packaging protein


Mass: 10628.258 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage Nocturne116 (virus) / References: UniProt: A0A8E5K7F6
#3: Protein
Major capsid protein


Mass: 57442.773 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Lactococcus phage Nocturne116 (virus) / References: UniProt: A0A8E5NR45
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

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1Lactococcus phage Nocturne116VIRUSall0NATURAL
2CapsidCOMPLEX#31NATURALProlate capsid composed of major head protein and vertex protein
3Portal complexCOMPLEX#1-#21NATURALComplex of 12 portal protein and 12 head-tail connector protein molecules
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Lactococcus phage Nocturne116 (virus)2831179
32Lactococcus phage Nocturne116 (virus)2831179
43Lactococcus 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 / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
7Coot0.9.8model fitting
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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20447 / Symmetry type: POINT
Atomic model buildingDetails: Previous reconstruction / Source name: Other / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001564826
ELECTRON MICROSCOPYf_angle_d0.325387814
ELECTRON MICROSCOPYf_chiral_restr0.038110425
ELECTRON MICROSCOPYf_plane_restr0.002311154
ELECTRON MICROSCOPYf_dihedral_angle_d2.83378802

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