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- EMDB-6324: Electron cryo-microscopy of T4 portal protein -

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Basic information

Entry
Database: EMDB / ID: EMD-6324
TitleElectron cryo-microscopy of T4 portal protein
Map dataReconstruction of T4 portal protein gp20
Sample
  • Sample: T4 portal protein gp20
  • Protein or peptide: T4 Portal protein gp20
KeywordsT4 portal protein
Function / homologyPortal protein Gp20 / Bacteriophage T4-like portal protein (Gp20) / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral portal complex / viral genome packaging / viral release from host cell / host cell plasma membrane / membrane / Portal protein
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSun L / Zhang X / Gao S / Rao PA / Padilla-Sanchez V / Chen Z / Sun S / Xiang Y / Sriram S / Rao VB / Rossmann MG
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.
Authors: Lei Sun / Xinzheng Zhang / Song Gao / Prashant A Rao / Victor Padilla-Sanchez / Zhenguo Chen / Siyang Sun / Ye Xiang / Sriram Subramaniam / Venigalla B Rao / Michael G Rossmann /
Abstract: The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage ...The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.
History
DepositionApr 21, 2015-
Header (metadata) releaseMay 6, 2015-
Map releaseJul 22, 2015-
UpdateJul 22, 2015-
Current statusJul 22, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3ja7
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3ja7
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6324.gif

Downloads & links

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Map

FileDownload / File: emd_6324.map.gz / Format: CCP4 / Size: 75 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of T4 portal protein gp20
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 272 pix.
= 272. Å		1 Å/pix.
x 272 pix.
= 272. Å		1 Å/pix.
x 272 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.09168965 - 0.13901675
Average (Standard dev.)0.00052522 (±0.00507363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-136-136-136
Dimensions272272272
Spacing272272272
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z272272272
origin x/y/z0.0000.0000.000
length x/y/z272.000272.000272.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS-136-136-136
NC/NR/NS272272272
D min/max/mean-0.0920.1390.001

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Supplemental data

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Sample components

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Entire : T4 portal protein gp20

EntireName: T4 portal protein gp20
Components
  • Sample: T4 portal protein gp20
  • Protein or peptide: T4 Portal protein gp20

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Supramolecule #1000: T4 portal protein gp20

SupramoleculeName: T4 portal protein gp20 / type: sample / ID: 1000 / Oligomeric state: dodecamer / Number unique components: 1
Molecular weightExperimental: 660 KDa

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Macromolecule #1: T4 Portal protein gp20

MacromoleculeName: T4 Portal protein gp20 / type: protein_or_peptide / ID: 1 / Name.synonym: connector / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage T4 (virus) / synonym: phage T4
Molecular weightExperimental: 660 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3) pLysS / Recombinant plasmid: pCDFDuet-1
SequenceUniProtKB: 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

Concentration1.0 mg/mL
BufferpH: 7.8 / Details: 20 mM Tris, 400 mM NaCl, 5 mM EDTA
GridDetails: Quantifoil R1.2/1.3 holey carbon on 200 mesh copper
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 7 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
Specialist opticsEnergy filter - Name: Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 25.0 eV
DateJul 10, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 839 / Average electron dose: 2 e/Å2
Details: Every image is the average of 11 frames recorded by the direct electron detector.
Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder: Liquid nitrogen-cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using an automatic selection program.
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 98000
Final two d classificationNumber classes: 15

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