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- EMDB-55367: Tail tip structure of Lactococcus phage Nocturne116 -

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Basic information

Entry
Database: EMDB / ID: EMD-55367
TitleTail tip structure of Lactococcus phage Nocturne116
Map data
Sample
  • Virus: Lactococcus phage Nocturne116 (virus)
    • Complex: Tail tube
      • Protein or peptide: Major tail shaft protein
    • Complex: Tail tip
      • Protein or peptide: Distal tail protein 1
      • Protein or peptide: Distal tail protein 2
      • Protein or peptide: Minor structural protein
      • Protein or peptide: Tail tape measure protein
KeywordsBacteriophage / tail / baseplate / VIRUS
Function / homology: / : / : / : / :
Function and homology information
Biological speciesLactococcus phage Nocturne116 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 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_55367.png

Downloads & links

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Map

FileDownload / File: emd_55367.map.gz / Format: CCP4 / Size: 282.6 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 420 pix.
= 328.86 Å		0.78 Å/pix.
x 420 pix.
= 328.86 Å		0.78 Å/pix.
x 420 pix.
= 328.86 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-0.015193088 - 0.029084876
Average (Standard dev.)0.000048560258 (±0.00081563875)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 328.86 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55367_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55367_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55367_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: Tail tube
      • Protein or peptide: Major tail shaft protein
    • Complex: Tail tip
      • Protein or peptide: Distal tail protein 1
      • Protein or peptide: Distal tail protein 2
      • Protein or peptide: Minor structural protein
      • Protein or peptide: Tail tape measure 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: Tail tube

SupramoleculeName: Tail tube / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Distal ring of six tail tube protein molecules
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)

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Supramolecule #3: Tail tip

SupramoleculeName: Tail tip / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Details: Complex of baseplate hub protein and two distal tail proteins
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)

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Macromolecule #1: Major tail shaft protein

MacromoleculeName: Major tail shaft protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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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Macromolecule #2: Distal tail protein 1

MacromoleculeName: Distal tail protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 13.755672 KDa
SequenceString:
MSIKIFKTTP AAMYVISNSE NVDIKPEGLE LCVAEIDDLI EPSGTFTLTL SENDPFLIQE NQLYTLRDEF GATKWSVNRA THITPFFVS SVRREFGIVK YECTKVYKSF LEMTGLYSGE LL

UniProtKB: UNIPROTKB: A0A8E5K7G7

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Macromolecule #3: Distal tail protein 2

MacromoleculeName: Distal tail protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 22.744648 KDa
SequenceString: MKKAKIEGWS LVDLWVDETP FQSDKSVNIY GFDAFPVLIK SWASQRDRLI ITIDEGNGAI SLFVAKSKRG NGYVGRKRES GELRVGRIF DIVSPIYYIK NPVRGDGSSP AVKYITTYSK DSDVKACMFF PTAVAELQVL VNGYTPGDEL TKTYGKGFGV A GTSTFYES ...String:
MKKAKIEGWS LVDLWVDETP FQSDKSVNIY GFDAFPVLIK SWASQRDRLI ITIDEGNGAI SLFVAKSKRG NGYVGRKRES GELRVGRIF DIVSPIYYIK NPVRGDGSSP AVKYITTYSK DSDVKACMFF PTAVAELQVL VNGYTPGDEL TKTYGKGFGV A GTSTFYES MSCEFSGEIA GFDSCQIRNT TDSTGATRAA YIGGEYQIL

UniProtKB: UNIPROTKB: A0A8E5K7K4

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Macromolecule #4: Minor structural protein

MacromoleculeName: Minor structural protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 42.565297 KDa
SequenceString: MTTHSLKLLH LQGRSTPWQN SPQVTVSVIQ DRWTFDKGRE IEFMAMGLPQ SFIFIVDSKI QDQEGQRAGD CRAGSWCGQA TRIGLNRYQ GIQASGTNNE ASGLIAFGTA NSTSFGKVST SNVSGIALGA NIDVALGQTA AANVSSGAVA DRMSFPEFGR P KTPNARIR ...String:
MTTHSLKLLH LQGRSTPWQN SPQVTVSVIQ DRWTFDKGRE IEFMAMGLPQ SFIFIVDSKI QDQEGQRAGD CRAGSWCGQA TRIGLNRYQ GIQASGTNNE ASGLIAFGTA NSTSFGKVST SNVSGIALGA NIDVALGQTA AANVSSGAVA DRMSFPEFGR P KTPNARIR TLAFGNAVDQ ATKTIRSGPS VVRRSMYEFG GDFATTQFYP RYDSNIAVGG VTYGSCYTAD YQGLPMGAIK AS ALPISEG KVSEKLDGDG RTAVWRVWAI AGAENLTPYK YHYLVMYVEA DGTLSFGAST GSTPNSTNGD SVFSEAYTIF SDD KFNTAN NSENQDILKQ AYYAAKTKSQ NFTVKRPIVV PNAFFPLTEK TQKGHLITQS WIISADFINH EYRIGE

UniProtKB: UNIPROTKB: A0A8E5K7F3

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Macromolecule #5: Tail tape measure protein

MacromoleculeName: Tail tape measure protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus phage Nocturne116 (virus)
Molecular weightTheoretical: 81.245172 KDa
SequenceString: MAKSYTINTT LDSKQVELGL RQVNSLITAT TREANSMNKA MKISGDFSAG VKGADGLKKA LSLAEDRSNS LRSSLSKAKM DGSSANTVA DLEAKLKRSD SEAQELKNSL AGINNEGKKG ETDLLGTFSK VGNIATGAIA VFNVLKDTVG AVVGTAVDMG K TFVNGFVS ...String:
MAKSYTINTT LDSKQVELGL RQVNSLITAT TREANSMNKA MKISGDFSAG VKGADGLKKA LSLAEDRSNS LRSSLSKAKM DGSSANTVA DLEAKLKRSD SEAQELKNSL AGINNEGKKG ETDLLGTFSK VGNIATGAIA VFNVLKDTVG AVVGTAVDMG K TFVNGFVS QYDTMATANL TLGNTLKDGK KGLEDYNNEI KKSPALVRAQ KSELDQMAAT ISSYSDTTGK DAFKIVNAIN AV GDSVGAN IEDQKGFTRA LGQAMTAGKL MAQDFNQMSQ TALGKQFKGA LIDAANAAQG VGRSAADMSK DLETGKVKAV ELS NVFGSD WTKKMQAVMQ NNTGLKTSAG MVNDALKQGK LTADDFKKAL GDDYLQKLTD AANANKQGAV TSETFRSAME EGTF TSDIL QAALGRLIEQ GEKVPQVFST FEQVKMSVQN AFYTGAVEAF MEKMVGSKDK LNEFGQSATE FAQNAGAQLG GALGT AAQK VSEFIDANGG IEGIFKTMTS WTDAAIGKFQ AFAEDILIVI GNLLSLTKGT AELEKMGFQV DQTTGMVVGW KARTDE AKK KQEDWNKKLS EMNQIMPTTT KEMEKAGKAS GNLEQTGDRG SKGLDKVGNS ADFATGKLWE ANQAANQAKE SVKDIQG TV YVDASGAVNQ LSWLIDWSDA ASSRLQGLSN NYGNMGRQFE LRAEGSELMH EGARGIERAS KAFGALEHYN AARVAQGM P APPQQNNSTV FGAGAIQIAV GAGANDNAIA ELEAKLRRLG IRIY

UniProtKB: UNIPROTKB: A0A8E5NR27

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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 correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: De novo initial model produced in Relion
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Number images used: 10559
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: Model produced using ModelAngelo
Output model

PDB-9sze:
Tail tip structure of Lactococcus phage Nocturne116

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