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- EMDB-4567: Viral pore protein -

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Basic information

Entry
Database: EMDB / ID: EMD-4567
TitleViral pore protein
Map data
Sample
  • Complex: Thermus phage P2345
    • Protein or peptide: Portal protein
Keywordsportal / translocase / motor / pore / bacteriophage / thermophage / caudovirales / siphoviridae / virus / VIRAL PROTEIN
Function / homology: / Barrel domain in phage portal protein / viral capsid / Portal protein
Function and homology information
Biological speciesThermus phage P2345 (virus) / Thermus virus P23-45
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsBayfield OW / Antson AA / Winkler DC / Hesketh EL / Chechik M / Cheng N / Dykeman EC / Minakhin L / Ranson NA / Severinov K / Steven AC
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust206377 United Kingdom
Wellcome Trust103460 United Kingdom
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structure in situ reveals a molecular switch that safeguards virus against genome loss.
Authors: Oliver W Bayfield / Alasdair C Steven / Alfred A Antson /
Abstract: The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is ...The portal protein is a key component of many double-stranded DNA viruses, governing capsid assembly and genome packaging. Twelve subunits of the portal protein define a tunnel, through which DNA is translocated into the capsid. It is unknown how the portal protein functions as a gatekeeper, preventing DNA slippage, whilst allowing its passage into the capsid, and how these processes are controlled. A cryo-EM structure of the portal protein of thermostable virus P23-45, determined in situ in its procapsid-bound state, indicates a mechanism that naturally safeguards the virus against genome loss. This occurs via an inversion of the conformation of the loops that define the constriction in the central tunnel, accompanied by a hydrophilic-hydrophobic switch. The structure also shows how translocation of DNA into the capsid could be modulated by a changing mode of protein-protein interactions between portal and capsid, across a symmetry-mismatched interface.
History
Header (metadata) releaseDec 5, 2018-
DepositionJan 24, 2019-
Map releaseMar 25, 2020-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.078
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.078
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qjt
  • Surface level: 0.078
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qjt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4567.png

Downloads & links

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Map

FileDownload / File: emd_4567.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 138 pix.
= 220.455 Å		1.6 Å/pix.
x 138 pix.
= 220.455 Å		1.6 Å/pix.
x 138 pix.
= 220.455 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.078 / Movie #1: 0.078
Minimum - Maximum-0.17127588 - 0.31609887
Average (Standard dev.)0.0033498895 (±0.027350517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions138138138
Spacing138138138
CellA=B=C: 220.455 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.59751.59751.5975
M x/y/z138138138
origin x/y/z0.0000.0000.000
length x/y/z220.455220.455220.455
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS138138138
D min/max/mean-0.1710.3160.003

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Supplemental data

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Mask #1

Fileemd_4567_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4567_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4567_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Thermus phage P2345

EntireName: Thermus phage P2345 (virus)
Components
  • Complex: Thermus phage P2345
    • Protein or peptide: Portal protein

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Supramolecule #1: Thermus phage P2345

SupramoleculeName: Thermus phage P2345 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus phage P2345 (virus)
Molecular weightTheoretical: 596 KDa

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermus virus P23-45
Molecular weightTheoretical: 49.714141 KDa
SequenceString: MAKRGRKPKE LVPGPGSIDP SDVPKLEGAS VPVMSTSYDV VVDREFDELL QGKDGLLVYH KMLSDGTVKN ALNYIFGRIR SAKWYVEPA STDPEDIAIA AFIHAQLGID DASVGKYPFG RLFAIYENAY IYGMAAGEIV LTLGADGKLI LDKIVPIHPF N IDEVLYDE ...String:
MAKRGRKPKE LVPGPGSIDP SDVPKLEGAS VPVMSTSYDV VVDREFDELL QGKDGLLVYH KMLSDGTVKN ALNYIFGRIR SAKWYVEPA STDPEDIAIA AFIHAQLGID DASVGKYPFG RLFAIYENAY IYGMAAGEIV LTLGADGKLI LDKIVPIHPF N IDEVLYDE EGGPKALKLS GEVKGGSQFV NGLEIPIWKT VVFLHNDDGS FTGQSALRAA VPHWLAKRAL ILLINHGLER FM IGVPTLT IPKSVRQGTK QWEAAKEIVK NFVQKPRHGI ILPDDWKFDT VDLKSAMPDA IPYLTYHDAG IARALGIDFN TVQ LNMGVQ AVNIGEFVSL TQQTIISLQR EFASAVNLYL IPKLVLPNWP GATRFPRLTF EMEERNDFSA AANLMGMLIN AVKD SEDIP TELKALIDAL PSKMRRALGV VDEVREAVRQ PADSRYLYTR RRR

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: 8
Component:
ConcentrationFormula
100.0 mMNaCl
20.0 mMTris-HCl
10.0 mMMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.0 sec. / Average electron dose: 99.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 10025
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6qjt:
Thermophage P23-45 in situ procapsid portal protein

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