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- EMDB-55363: Asymmetric structure of the capsid-portal complex of Lactococcus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-55363
TitleAsymmetric structure of the capsid-portal complex of Lactococcus phage Nocturne116
Map data
Sample
  • Virus: Lactococcus phage Nocturne116 (virus)
    • Complex: Capsid
      • Protein or peptide: Major capsid protein
    • Complex: Portal complex
      • Protein or peptide: Putative portal protein
      • Protein or peptide: DNA packaging protein
KeywordsBacteriophage / capsid / portal / VIRUS
Function / homology: / : / :
Function and homology information
Biological speciesLactococcus phage Nocturne116 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 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_55363.png

Downloads & links

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Map

FileDownload / File: emd_55363.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 281.88 Å		0.78 Å/pix.
x 360 pix.
= 281.88 Å		0.78 Å/pix.
x 360 pix.
= 281.88 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: 0.014
Minimum - Maximum-0.039986137 - 0.06522545
Average (Standard dev.)0.00029378216 (±0.0033664936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 281.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55363_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55363_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_55363_half_map_2.map
Projections & Slices
AxesZYX

Projections

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: Capsid
      • Protein or peptide: Major capsid protein
    • Complex: Portal complex
      • Protein or peptide: Putative portal protein
      • Protein or peptide: DNA packaging 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: Capsid

SupramoleculeName: Capsid / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Details: Prolate capsid composed of major head protein and vertex protein
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)

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Supramolecule #3: Portal complex

SupramoleculeName: Portal complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Details: Complex of 12 portal protein and 12 head-tail connector protein molecules
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: 12 / 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: 12 / 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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 57.442773 KDa
SequenceString: MKASFNDRVL EGKLVDYNSI DSFKSVISEG AFDDDVQSGK TYNLDYRHNV YDVLATFKTE KREDGIYITA EPKDEQSYQR MREEVAAGA GLSVMFAPTE ATEGDGITFY KKARLVGGAL TRQPSNKNAV VTYFREENKE KENENMTIDT QLMEEVLKLR A ENETLKTR ...String:
MKASFNDRVL EGKLVDYNSI DSFKSVISEG AFDDDVQSGK TYNLDYRHNV YDVLATFKTE KREDGIYITA EPKDEQSYQR MREEVAAGA GLSVMFAPTE ATEGDGITFY KKARLVGGAL TRQPSNKNAV VTYFREENKE KENENMTIDT QLMEEVLKLR A ENETLKTR SAAPVNPELA EVTNLAKELL KSRETEKIVG VEALKVATPE AAEWLKTREA EVKYMEASLS NDPLEHWKET LK ARSITGI PAPTGILKKI HDIVNDRNSI LAYIRHENLP TLTVGGDKAL SKGEGHTAGT DKNESEIQLE TRVLTPQYVY KYI KLPKLV MNKNASEIAG ALLTYVLNRL PQMVIFAVNR AIIMGDVTGV SKTQIYPVVG DTWATNVGEK ETVIDLIETL SVST PKAYD SSLVISRADW SAVRFTKDKN GRERFLGLSD AELANHFGFE RVLITTAVDA GTIVSLDGYV TNGSRGMEFE EGRIL VENN KEYLFEMPIS GSLEYKEMAA YGTIKKPVTG GE

UniProtKB: UNIPROTKB: A0A8E5NR45

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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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: 3D class after symmetry expansion of previous reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 20447
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: Previous reconstruction
Output model

PDB-9sza:
Asymmetric structure of the capsid-portal complex of Lactococcus phage Nocturne116

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