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- EMDB-20960: In situ C12 reconstruction of phage T4 portal protein assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-20960
TitleIn situ C12 reconstruction of phage T4 portal protein assembly
Map dataC12 reconstruction of phage T4 portal protein assembly
Sample
  • Virus: Escherichia virus T4
Biological speciesEscherichia virus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFang Q / Fokine A / Rossmann MG / Rao VB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases 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 15, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseApr 22, 2020-
UpdateApr 22, 2020-
Current statusApr 22, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20960.png

Downloads & links

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Map

FileDownload / File: emd_20960.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC12 reconstruction of phage T4 portal protein assembly
Voxel sizeX=Y=Z: 1.44 Å
Density
Contour LevelBy AUTHOR: 0.22 / Movie #1: 0.22
Minimum - Maximum-0.7064607 - 1.0020752
Average (Standard dev.)0.0028884304 (±0.055601384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100241
Dimensions200200200
Spacing200200200
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.441.441.44
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z288.000288.000288.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100241
NC/NR/NS200200200
D min/max/mean-0.7061.0020.003

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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

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Supramolecule #1: Escherichia virus T4

SupramoleculeName: Escherichia virus T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / 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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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

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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: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53608

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