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- EMDB-62433: The Composite Cryo-EM Structure of the Portal Vertex of Bacteriop... -

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Basic information

Entry
Database: EMDB / ID: EMD-62433
TitleThe Composite Cryo-EM Structure of the Portal Vertex of Bacteriophage FCWL1
Map data
Sample
  • Virus: Escherichia phage FCWL1 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Decoration protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Terminator protein
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Connector protein
    • Protein or peptide: Decoration protein gp29
KeywordsT1-like phage / capsid / icosahedrally averaged / VIRAL PROTEIN
Function / homology
Function and homology information


Phage tail tube protein 3 / Protein of unknown function DUF2184 / Phage tail tube protein, TTP / Major capsid protein / Protein of unknown function DUF4128 / Phage tail terminator protein / Protein of unknown function DUF4054 / : / Protein of unknown function (DUF4054) / Structural cement protein (E217 gp24/Pam3 gp6) ...Phage tail tube protein 3 / Protein of unknown function DUF2184 / Phage tail tube protein, TTP / Major capsid protein / Protein of unknown function DUF4128 / Phage tail terminator protein / Protein of unknown function DUF4054 / : / Protein of unknown function (DUF4054) / Structural cement protein (E217 gp24/Pam3 gp6) / Protein of unknown function DUF1073 / Phage portal protein / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Major capsid protein / IgG-domain-containing decoration protein / Portal protein / Terminator protein / Decoration protein / Adaptor protein / Tail tube protein / Connector protein
Similarity search - Component
Biological speciesEscherichia phage FCWL1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCai C / Wang Y / Liu Y / Shao Q / Wang A / Fang Q
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
DepositionNov 16, 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_62433.png

Downloads & links

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Map

FileDownload / File: emd_62433.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 320 pix.
= 515.52 Å		1.61 Å/pix.
x 320 pix.
= 515.52 Å		1.61 Å/pix.
x 320 pix.
= 515.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.611 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.36
Minimum - Maximum-10.394235 - 17.657067999999999
Average (Standard dev.)0.0074350196 (±1.0761553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 515.51996 Å
α=β=γ: 90.0 °

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Supplemental data

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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: Major capsid protein
    • Protein or peptide: Decoration protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Terminator protein
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Connector protein
    • Protein or peptide: Decoration protein gp29

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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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 35.301375 KDa
SequenceString: MTTKKFDEAD KSNVEMYLIQ AGVKQDAAAT MGIWTAQELH RIKSQSYEED YPVGSALRVF PVTTELSPTD KTFEYMTFDK VGTAQIIAD YTDDLPLVDA LGTSEFGKVF RLGNAYLISI DEIKAGQATG RPLSTRKASA CQLAHDQLVN RLVFKGSAPH K IVSVFNHP ...String:
MTTKKFDEAD KSNVEMYLIQ AGVKQDAAAT MGIWTAQELH RIKSQSYEED YPVGSALRVF PVTTELSPTD KTFEYMTFDK VGTAQIIAD YTDDLPLVDA LGTSEFGKVF RLGNAYLISI DEIKAGQATG RPLSTRKASA CQLAHDQLVN RLVFKGSAPH K IVSVFNHP NITKITSGKW IDASTMKPET AEAELTQAIE TIETITRGQH RATNILIPPS MRKVLAIRMP ETTMSYLDYF KS QNSGIEI DSIAELEDID GAGTKGVLVY EKNPMNMSIE IPEAFNMLPA QPKDLHFKVP CTSKCTGLTI YRPMTIVLIT GV

UniProtKB: Major capsid protein

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Macromolecule #2: Decoration protein

MacromoleculeName: Decoration protein / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 17.022135 KDa
SequenceString:
MAQINASYQR DMAIALPGMV ADTSKYNIDG ACVVNEGDVL VGAAVQVVQA QAVDGHKLVK ALTTGTTPYG VAIRSHWQTV NAQNQMIYE DGGAINVMTS GRVWMLSKST EAPTFGSAVK LDVDGQEKSD GTIETTWTYA GGWTKYKDIQ LVEVQLHQL

UniProtKB: Decoration protein

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Macromolecule #3: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / 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: Terminator protein

MacromoleculeName: Terminator protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / 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 #5: Adaptor protein

MacromoleculeName: Adaptor protein / type: protein_or_peptide / ID: 5 / Number of copies: 12 / 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 #6: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 6 / Number of copies: 6 / 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 #7: Connector protein

MacromoleculeName: Connector protein / type: protein_or_peptide / ID: 7 / Number of copies: 6 / 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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Macromolecule #8: Decoration protein gp29

MacromoleculeName: Decoration protein gp29 / type: protein_or_peptide / ID: 8 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage FCWL1 (virus)
Molecular weightTheoretical: 26.355309 KDa
SequenceString: MAYENLFLRP ACPGNISDTS TYNIDGACVA QGDIGFGSAV QVVGIVDGVK VVAALPDGGT PYGIAFRSQY EHLSGKILDG EVCNVVSHG RVWTLTSLGE APSLFSKLQF GSGGVVTGGS GSAGWTFAGG FVKHEDGYII EVQVKQNAFI APPPPPPVVL V ESATIATD ...String:
MAYENLFLRP ACPGNISDTS TYNIDGACVA QGDIGFGSAV QVVGIVDGVK VVAALPDGGT PYGIAFRSQY EHLSGKILDG EVCNVVSHG RVWTLTSLGE APSLFSKLQF GSGGVVTGGS GSAGWTFAGG FVKHEDGYII EVQVKQNAFI APPPPPPVVL V ESATIATD KESPQPNNVT IQCVANALPD NATDKTGKWS IDATNIATVD PDSGLVTPVG GEVVGDFNIT WTANDASKTT AT IAYRVEA VPTPEVDA

UniProtKB: IgG-domain-containing decoration 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
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Number images used: 74400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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