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- EMDB-61588: Cryo-EM Structure of Bacteriophage FCWL1 head-to-tail interface -

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Basic information

Entry
Database: EMDB / ID: EMD-61588
TitleCryo-EM Structure of Bacteriophage FCWL1 head-to-tail interface
Map data
Sample
  • Virus: Escherichia phage FCWL1 (virus)
    • Protein or peptide: Terminator protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Connector protein
KeywordsT1-like phage / neck / tail / VIRAL PROTEIN
Function / homology
Function and homology information


Phage tail tube protein 3 / Phage tail tube protein, TTP / Protein of unknown function DUF4128 / Phage tail terminator protein / Protein of unknown function DUF4054 / Protein of unknown function (DUF4054) / Protein of unknown function DUF1073 / Phage portal protein
Similarity search - Domain/homology
Portal protein / Terminator protein / Adaptor protein / Tail tube protein / Connector protein
Similarity search - Component
Biological speciesEscherichia phage FCWL1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCai C / Wang Y / Liu Y / Shao Q / Wang A / Fang Q / Zheng Y / Zhang T / Luo Z / Yang C
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentD2301008
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: Structure / Year: 2025
Title: Structures of a T1-like siphophage reveal capsid stabilization mechanisms and high structural similarities with a myophage.
Authors: Can Cai / Yueting Wang / Yunshu Liu / Qianqian Shao / Aohan Wang / Lin Li / Yaqi Zheng / Tianyi Zhang / Ziwen Luo / Chongguang Yang / Qianglin Fang /
Abstract: Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1- ...Bacteriophage T1, a member of Siphoviruses, infects Escherichia coli with high efficiency, making it a promising candidate for phage therapy. Here, we report the near-atomic structures of FCWL1, a T1-like phage that belongs to the T1 phage family. We focus on the head, the head-to-tail interface, and its surrounding components. The hexameric capsomer displays unique gaps between neighboring A domains of the major capsid proteins. These gaps are partially filled by the N-loop of the decoration protein, which adopts a unique conformation. These structural features suggest that the phage might employ a novel strategy for stabilizing its head. Furthermore, despite being a siphophage, the head and head-to-tail connector of the phage show high structural similarity to those of a myophage. These findings enhance our understanding of the structure, capsid stabilization mechanism, and evolution of phages in the T1 family.
History
DepositionSep 18, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61588.png

Downloads & links

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Map

FileDownload / File: emd_61588.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 400 pix.
= 515.52 Å		1.29 Å/pix.
x 400 pix.
= 515.52 Å		1.29 Å/pix.
x 400 pix.
= 515.52 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2888 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.054781955 - 0.09494707
Average (Standard dev.)-0.000020140793 (±0.0028847065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 515.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61588_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_61588_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61588_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage FCWL1

EntireName: Escherichia phage FCWL1 (virus)
Components
  • Virus: Escherichia phage FCWL1 (virus)
    • Protein or peptide: Terminator protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Connector protein

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Supramolecule #1: Escherichia phage FCWL1

SupramoleculeName: Escherichia phage FCWL1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3136680 / Sci species name: Escherichia phage FCWL1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Terminator protein

MacromoleculeName: Terminator protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 15.191521 KDa
SequenceString:
MHYELSAAAR AAFLSKYRDF PHYMENRNFT PPKDGGMWLR FNYIEGDTLY LSIDRKCKSY IAIVQIGVVF PPGSGVDEAR LKAKEIADF FKDGKMLNVG YIFEGAIVHQ IVKHESGWMI PVRFTVRVDT KET

UniProtKB: Terminator protein

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Macromolecule #2: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 24.21718 KDa
SequenceString: MHLPNGAQIF VETSRGEEIE ATAVTNEKNP VATVASKGDL AKGDYVIVTQ STWAKMVSRV LIVTDAQETS ITLAGIDTSD TLVFPAGGT MSFAKITGWT EIPCVQEIGQ DGGEQQYYTY QCLSDDKEQQ IPTFKSAISL TYTFAHEFDN PIYQILRKLD S SGQVTAVR ...String:
MHLPNGAQIF VETSRGEEIE ATAVTNEKNP VATVASKGDL AKGDYVIVTQ STWAKMVSRV LIVTDAQETS ITLAGIDTSD TLVFPAGGT MSFAKITGWT EIPCVQEIGQ DGGEQQYYTY QCLSDDKEQQ IPTFKSAISL TYTFAHEFDN PIYQILRKLD S SGQVTAVR MYVPKASEMR MWAGILSFND IPSTQVNEME TVELAVSLKG DFTFISSTLA SPGA

UniProtKB: Tail tube protein

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Macromolecule #3: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 49.969102 KDa
SequenceString: MRYNQGCQLT AFFIGGNMKI VKHDGYNDIF NGGADGSPKP FFMSDASYHV GSFYNDNATA KRIVDVIPEE MVTAGFKISG VKDEKEFKS LWDSYKIDPS LVDALCWARL YGGAAIVAII NDNRMLTSPV KPGAKLEGVR VYDRFAITIE KRVTNARSPR Y GEPEIYKV ...String:
MRYNQGCQLT AFFIGGNMKI VKHDGYNDIF NGGADGSPKP FFMSDASYHV GSFYNDNATA KRIVDVIPEE MVTAGFKISG VKDEKEFKS LWDSYKIDPS LVDALCWARL YGGAAIVAII NDNRMLTSPV KPGAKLEGVR VYDRFAITIE KRVTNARSPR Y GEPEIYKV SPGDNIQPYL IHHTRIFIAD GERVTPQMRK QNQGWGASVL NKSLIDAICD YDYCESLATQ ILRRKQQAVW KV KGLAEMC DDDDAQYAAR LRLAQVDDNS GVGRAIGIDA ETEEYDVLNS DISGVPEFLS SKMDRIVSLS GIHEIIIKNK NVG GVSASQ NTALETFYKL VDRKREEDYR PLLEFLLPFI VDEQEWSIEF EPLSVPSKKE ESEITKNNVE SVTKAITEQI IDLE EARDT LRSIAPEFKL KDGNNINIRE PEEPTEPEPG LGEKLEDEN

UniProtKB: Portal protein

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Macromolecule #4: Adaptor protein

MacromoleculeName: Adaptor protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 15.827354 KDa
SequenceString:
MGVIMNQETL IAAVEQMRKL VPALRKVPDE TLYAWVEMAE LFVCQKTFKD AYVKAIALYA LHLAFLDGAL KGEDEDLESY SRRVTSFSL SGEFSQTFGE VTKNQSGNMM LSTPWGKMFE QLKARRRGRF ALMTGLRGGC H

UniProtKB: Adaptor protein

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Macromolecule #5: Connector protein

MacromoleculeName: Connector protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 13.831523 KDa
SequenceString:
MNYSQIERMA RKGVAFFTDP SRPMNLIKQG EYGYDENGFE IPPMEQVIPI SGATRRPNAR EIDGETIRAS DILGIFNNDH EINEGDYIE IDGIRHVVVD ARPVQASLEP VAYRPVLRRV SVGG

UniProtKB: Connector protein

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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

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 25.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 84600
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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