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- EMDB-55365: Neck structure of Lactococcus phage Nocturne116 -

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Basic information

Entry
Database: EMDB / ID: EMD-55365
TitleNeck structure of Lactococcus phage Nocturne116
Map data
Sample
  • Virus: Lactococcus phage Nocturne116 (virus)
    • Complex: Neck
      • Protein or peptide: Putative portal protein
      • Protein or peptide: DNA packaging protein
      • Protein or peptide: Structural protein 2
      • Protein or peptide: Tail terminator protein
      • Protein or peptide: Major tail shaft protein
KeywordsBacteriophage / neck / head-tail connector / VIRUS
Function / homology: / : / : / : / :
Function and homology information
Biological speciesLactococcus phage Nocturne116 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsRumnieks J / Tars K
Funding supportEuropean Union, 2 items
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, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55365.png

Downloads & links

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Map

FileDownload / File: emd_55365.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 448 pix.
= 350.784 Å		0.78 Å/pix.
x 448 pix.
= 350.784 Å		0.78 Å/pix.
x 448 pix.
= 350.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.783 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.02201922 - 0.034263708
Average (Standard dev.)0.000037118447 (±0.0010000835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 350.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55365_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55365_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55365_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Lactococcus phage Nocturne116

EntireName: Lactococcus phage Nocturne116 (virus)
Components
  • Virus: Lactococcus phage Nocturne116 (virus)
    • Complex: Neck
      • Protein or peptide: Putative portal protein
      • Protein or peptide: DNA packaging protein
      • Protein or peptide: Structural protein 2
      • Protein or peptide: Tail terminator protein
      • Protein or peptide: Major tail shaft protein

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Supramolecule #1: Lactococcus phage Nocturne116

SupramoleculeName: Lactococcus phage Nocturne116 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2831179 / Sci species name: Lactococcus phage Nocturne116 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Lactococcus lactis (lactic acid bacteria) / Strain: LNT

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Supramolecule #2: Neck

SupramoleculeName: Neck / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)

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Macromolecule #1: Putative portal protein

MacromoleculeName: Putative portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 35.015707 KDa
SequenceString: MGIFKKREAA QPVPQTVNTI NQVTIKDNTI VAAIDFNVRN EVAESVSSYL GAYSLSSDRL SKITNNTSFL HRLVKHVLKH EQTFIYNSE TYGWVMTDTV VLNQTRVTMT IQLPNPYNSS IYLSVPLKDV GVIDTTMMNV DTEAANKMLE AAYEAVIKKL N NTGAIKAF ...String:
MGIFKKREAA QPVPQTVNTI NQVTIKDNTI VAAIDFNVRN EVAESVSSYL GAYSLSSDRL SKITNNTSFL HRLVKHVLKH EQTFIYNSE TYGWVMTDTV VLNQTRVTMT IQLPNPYNSS IYLSVPLKDV GVIDTTMMNV DTEAANKMLE AAYEAVIKKL N NTGAIKAF ISSNVDVGLN KMAEDANDKI KTMLKTASEL AGYTFLNKGD EVTQMMPDYT TSNTADFAAM RAFAASQLSV SE KILDGSA TDGEKVAVMF RFLDPILQQF KEYEPTLNYS IRDEMFVAFM TTGGLLNSNK IEYWGKEKTI NDRASQV

UniProtKB: UNIPROTKB: A0A8E5NQ91

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Macromolecule #2: DNA packaging protein

MacromoleculeName: DNA packaging protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 10.628258 KDa
SequenceString:
MVTILEQAAR QARVSTSILE SVIDNSIFRL KTAGVIVKAD DEYLPNELLP IVVQFIAIDA RITLLGDELW APSVANMQQK RQGLINTIE LLSKGNE

UniProtKB: UNIPROTKB: A0A8E5K7F6

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Macromolecule #3: Structural protein 2

MacromoleculeName: Structural protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 10.03325 KDa
SequenceString:
MEVASLKDFI INNETVMATV VGESSKYVNN EDSLNPQLVK SWLLRMSGPI FAETVTDKST NDEYLVTKTY TKLGYTYFEV TERNNAFL

UniProtKB: UNIPROTKB: A0A8E5K7D1

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Macromolecule #4: Tail terminator protein

MacromoleculeName: Tail terminator protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 12.223663 KDa
SequenceString:
MIDSSVKNLK DIITKNFNEG RVSNSADYKG QNFSFSMPSF QGSNAAIEKI TILTIFAIND FYVSDILERL SEESIDMSIE FTGMSGNYA TYQVLMRKSI DEKGETDLW

UniProtKB: UNIPROTKB: A0A8E5K7E4

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Macromolecule #5: Major tail shaft protein

MacromoleculeName: Major tail shaft protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 23.718643 KDa
SequenceString: MVENILTKTA YHGFGRVIVF PIANGVHGTG LPMLGGRSMD KKPEQTITTI GADMDGVYMA KTGSAVTQLE LKTIGKIPAD FKTKCLGFG GIGDADSEAF IDDPSATNPY GIAFAQWVDE DPGTQKIRVQ IYYSLAGTTP TETNEYDDPT GEASITEFTF T ATAQGFAG ...String:
MVENILTKTA YHGFGRVIVF PIANGVHGTG LPMLGGRSMD KKPEQTITTI GADMDGVYMA KTGSAVTQLE LKTIGKIPAD FKTKCLGFG GIGDADSEAF IDDPSATNPY GIAFAQWVDE DPGTQKIRVQ IYYSLAGTTP TETNEYDDPT GEASITEFTF T ATAQGFAG AVYEGVNRSF LEFTVDMTKT DSQAYKMYDQ IYTKKKILLP SEVAGLVPTP GE

UniProtKB: UNIPROTKB: A0A8E5K7E1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMsodium chlorideNaCl
10.0 mMmagnesium sulfateMgSO4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Symmetry relaxation of previous reconstruction
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 27997
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model produced using ModelAngelo
Output model

PDB-9szc:
Neck structure of Lactococcus phage Nocturne116

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