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- EMDB-32109: The expanded head structure of phage T4 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32109
TitleThe expanded head structure of phage T4
Map data
Sample
  • Virus: Escherichia virus T4
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid vertex protein
    • Protein or peptide: Small outer capsid protein
Function / homology
Function and homology information


viral capsid, decoration / T=13 icosahedral viral capsid / viral capsid
Similarity search - Function
Highly immunogenic outer capsid protein / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Capsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain ...Highly immunogenic outer capsid protein / Small outer capsid protein / Small outer capsid protein superfamily / Small outer capsid protein / Capsid vertex protein / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / PKD domain / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Highly immunogenic outer capsid protein / Small outer capsid protein / Major capsid protein / Capsid vertex protein
Similarity search - Component
Biological speciesBacteriophage T4 (virus) / Escherichia virus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFang Q / Tang W / Fokine A / Mahalingam M / Shao Q / Rossmann MG / Rao VB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
National Science Foundation (NSF, United States)MCB-0923873 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly.
Authors: Qianglin Fang / Wei-Chun Tang / Andrei Fokine / Marthandan Mahalingam / Qianqian Shao / Michael G Rossmann / Venigalla B Rao /
Abstract: Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that ...Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that transforms an immature unexpanded head into a mature genome-packaging head. Bacteriophage T4 is a model virus, well studied genetically and biochemically, but its structure determination has been challenging because of its large size and unusually prolate-shaped, ∼1,200-Å-long and ∼860-Å-wide capsid. Here, we report the cryogenic electron microscopy (cryo-EM) structures of T4 capsid in both of its major conformational states: unexpanded at a resolution of 5.1 Å and expanded at a resolution of 3.4 Å. These are among the largest structures deposited in Protein Data Bank to date and provide insights into virus assembly, head length determination, and shell expansion. First, the structures illustrate major domain movements and ∼70% additional gain in inner capsid volume, an essential transformation to contain the entire viral genome. Second, intricate intracapsomer interactions involving a unique insertion domain dramatically change, allowing the capsid subunits to rotate and twist while the capsomers remain fastened at quasi-threefold axes. Third, high-affinity binding sites emerge for a capsid decoration protein that clamps adjacent capsomers, imparting extraordinary structural stability. Fourth, subtle conformational changes at capsomers' periphery modulate intercapsomer angles between capsomer planes that control capsid length. Finally, conformational changes were observed at the symmetry-mismatched portal vertex, which might be involved in triggering head expansion. These analyses illustrate how small changes in local capsid subunit interactions lead to profound shifts in viral capsid morphology, stability, and volume.
History
DepositionOct 25, 2021-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32109.png

Downloads & links

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Map

FileDownload / File: emd_32109.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.44 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.7445007 - 0.98975044
Average (Standard dev.)0.00020801638 (±0.030558364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-480-480-480
Dimensions960960960
Spacing960960960
CellA=B=C: 1382.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Escherichia virus T4

EntireName: Escherichia virus T4
Components
  • Virus: Escherichia virus T4
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid vertex protein
    • Protein or peptide: Small outer capsid protein

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Supramolecule #1: Escherichia virus T4

SupramoleculeName: Escherichia virus T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10665 / Sci species name: Escherichia virus T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
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: 186 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage T4 (virus)
Molecular weightTheoretical: 56.074242 KDa
SequenceString: MTIKTKAELL NKWKPLLEGE GLPEIANSKQ AIIAKIFENQ EKDFQTAPEY KDEKIAQAFG SFLTEAEIGG DHGYNATNIA AGQTSGAVT QIGPAVMGMV RRAIPNLIAF DICGVQPMNS PTGQVFALRA VYGKDPVAAG AKEAFHPMYG PDAMFSGQGA A KKFPALAA ...String:
MTIKTKAELL NKWKPLLEGE GLPEIANSKQ AIIAKIFENQ EKDFQTAPEY KDEKIAQAFG SFLTEAEIGG DHGYNATNIA AGQTSGAVT QIGPAVMGMV RRAIPNLIAF DICGVQPMNS PTGQVFALRA VYGKDPVAAG AKEAFHPMYG PDAMFSGQGA A KKFPALAA STQTTVGDIY THFFQETGTV YLQASVQVTI DAGATDAAKL DAEIKKQMEA GALVEIAEGM ATSIAELQEG FN GSTDNPW NEMGFRIDKQ VIEAKSRQLK AAYSIELAQD LRAVHGMDAD AELSGILATE IMLEINREVV DWINYSAQVG KSG MTLTPG SKAGVFDFQD PIDIRGARWA GESFKALLFQ IDKEAVEIAR QTGRGEGNFI IASRNVVNVL ASVDTGISYA AQGL ATGFS TDTTKSVFAG VLGGKYRVYI DQYAKQDYFT VGYKGPNEMD AGIYYAPYVA LTPLRGSDPK NFQPVMGFKT RYGIG INPF AESAAQAPAS RIQSGMPSIL NSLGKNAYFR RVYVKGI

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Macromolecule #2: Capsid vertex protein

MacromoleculeName: Capsid vertex protein / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage T4 (virus)
Molecular weightTheoretical: 47.039023 KDa
SequenceString: MAKINELLRE STTTNSNSIG RPNLVALTRA TTKLIYSDIV ATQRTNQPVA AFYGIKYLNP DNEFTFKTGA TYAGEAGYVD REQITELTE ESKLTLNKGD LFKYNNIVYK VLEDTPFATI EESDLELALQ IAIVLLKVRL FSDAASTSKF ESSDSEIADA R FQINKWQT ...String:
MAKINELLRE STTTNSNSIG RPNLVALTRA TTKLIYSDIV ATQRTNQPVA AFYGIKYLNP DNEFTFKTGA TYAGEAGYVD REQITELTE ESKLTLNKGD LFKYNNIVYK VLEDTPFATI EESDLELALQ IAIVLLKVRL FSDAASTSKF ESSDSEIADA R FQINKWQT AVKSRKLKTG ITVELAQDLE ANGFDAPNFL EDLLATEMAD EINKDILQSL ITVSKRYKVT GITDSGFIDL SY ASAPEAG RSLYRMVCEM VSHIQKESTY TATFCVASAR AAAILAASGW LKHKPEDDKY LSQNAYGFLA NGLPLYCDTN SPL DYVIVG VVENIGEKEI VGSIFYAPYT EGLDLDDPEH VGAFKVVVDP ESLQPSIGLL VRYALSANPY TVAKDEKEAR IIDG GDMDK MAGRSDLSVL LGVKLPKIII DE

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Macromolecule #3: Small outer capsid protein

MacromoleculeName: Small outer capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 172 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage T4 (virus)
Molecular weightTheoretical: 9.085095 KDa
SequenceString:
MASARGYVNI KTFEQKLDGN KKIEGKEVSV AFPLYSDVHK ISGAHYQTFP SEKAAYSTVY EENQRTEWIA ANEDLWKVTG

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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: 7.5
VitrificationCryogen name: NITROGEN / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 23.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53608

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