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- EMDB-20956: Portal vertex structure of bacteriophage T4 -

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Basic information

Entry
Database: EMDB / ID: EMD-20956
TitlePortal vertex structure of bacteriophage T4
Map datalow-pass filtered and B-factor sharpened map
Sample
  • Virus: Escherichia virus T4
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein
Keywordsportal protein assembly / gp20 / gp23 / portal vertex / VIRUS
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / T=13 icosahedral viral capsid / viral portal complex / viral genome packaging / viral release from host cell / viral capsid / host cell plasma membrane / membrane
Similarity search - Function
Portal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / Major capsid protein, Myoviridae / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like
Similarity search - Domain/homology
Major capsid protein / Portal protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus) / Escherichia virus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsFang Q / Fokine A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural morphing in a symmetry-mismatched viral vertex.
Authors: Qianglin Fang / Wei-Chun Tang / Pan Tao / Marthandan Mahalingam / Andrei Fokine / Michael G Rossmann / Venigalla B Rao /
Abstract: Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of ...Large biological structures are assembled from smaller, often symmetric, sub-structures. However, asymmetry among sub-structures is fundamentally important for biological function. An extreme form of asymmetry, a 12-fold-symmetric dodecameric portal complex inserted into a 5-fold-symmetric capsid vertex, is found in numerous icosahedral viruses, including tailed bacteriophages, herpesviruses, and archaeal viruses. This vertex is critical for driving capsid assembly, DNA packaging, tail attachment, and genome ejection. Here, we report the near-atomic in situ structure of the symmetry-mismatched portal vertex from bacteriophage T4. Remarkably, the local structure of portal morphs to compensate for symmetry-mismatch, forming similar interactions in different capsid environments while maintaining strict symmetry in the rest of the structure. This creates a unique and unusually dynamic symmetry-mismatched vertex that is central to building an infectious virion.
History
DepositionNov 14, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uzc
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6uzc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20956.png

Downloads & links

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Map

FileDownload / File: emd_20956.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlow-pass filtered and B-factor sharpened map
Voxel sizeX=Y=Z: 1.44 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-18.706944 - 30.373089
Average (Standard dev.)0.019396635 (±0.6027698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250100
Dimensions500500500
Spacing500500500
CellA=B=C: 720.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.441.441.44
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z720.000720.000720.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS-250-250100
NC/NR/NS500500500
D min/max/mean-18.70730.3730.019

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Supplemental data

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Additional map: unfiltered map

Fileemd_20956_additional_1.map
Annotationunfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: emd 20956 additional 2.map

Fileemd_20956_additional_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 : Escherichia virus T4

EntireName: Escherichia virus T4
Components
  • Virus: Escherichia virus T4
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal 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: OTHER / Virus enveloped: No / Virus empty: Yes

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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: Enterobacteria phage 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

UniProtKB: Major capsid protein

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Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 61.117082 KDa
SequenceString: MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK ...String:
MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK EGIKELRRLD PRQVQYVREI ITETEAGTKI VKGYKEYFIY DTAHESYACD GRMYEAGTKI KIPKAAVVYA HS GLVDCCG KNIIGYLHRA VKPANQLKLL EDAVVIYRIT RAPDRRVWYV DTGNMPARKA AEHMQHVMNT MKNRVVYDAS TGK IKNQQH NMSMTEDYWL QRRDGKAVTE VDTLPGADNT GNMEDIRWFR QALYMALRVP LSRIPQDQQG GVMFDSGTSI TRDE LTFAK FIRELQHKFE EVFLDPLKTN LLLKGIITED EWNDEINNIK IEFHRDSYFA ELKEAEILER RINMLTMAEP FIGKY ISHR TAMKDILQMT DEEIEQEAKQ IEEESKEARF QDPDQEQEDF

UniProtKB: Portal 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
VitrificationCryogen name: ETHANE / 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

Startup modelType of model: EMDB MAP
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53608

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6uzc:
Portal vertex structure of bacteriophage T4

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