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- EMDB-0618: Icosahedral reconstruction of the thermophilic bacteriophage P74-... -

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Basic information

Entry
Database: EMDB / ID: EMD-0618
TitleIcosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid
Map dataIcosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid
Sample
  • Virus: Thermus phage P7426 (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: P74-26 Head Decoration Protein
KeywordsVirus / Virion / Capsid / Major Capsid Protein / Decoration Protein / Icosahedral Virus / Caudovirus / Thermophilic / Bacteriophage
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / host cell cytoplasm / Uncharacterized protein / Major head protein
Function and homology information
Biological speciesThermus virus P74-26 / Thermus phage P7426 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsStone NP / Demo G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nat Commun / Year: 2019
Title: Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure.
Authors: Nicholas P Stone / Gabriel Demo / Emily Agnello / Brian A Kelch /
Abstract: The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To ...The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.
History
DepositionFeb 26, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseJul 24, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 12.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6o3h
  • Surface level: 12.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6o3h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0618.png

Downloads & links

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Map

FileDownload / File: emd_0618.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 12.5 / Movie #1: 12.5
Minimum - Maximum-7.5911107 - 32.043087
Average (Standard dev.)0.111731134 (±4.700796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions102410241024
Spacing102410241024
CellA=B=C: 1084.416 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z1084.4161084.4161084.416
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS102410241024
D min/max/mean-7.59132.0430.112

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Supplemental data

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Sample components

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Entire : Thermus phage P7426

EntireName: Thermus phage P7426 (virus)
Components
  • Virus: Thermus phage P7426 (virus)
    • Protein or peptide: Major head protein
    • Protein or peptide: P74-26 Head Decoration Protein

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Supramolecule #1: Thermus phage P7426

SupramoleculeName: Thermus phage P7426 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 466052 / Sci species name: Thermus phage P7426 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Thermus thermophilus (bacteria) / Strain: HB8
Virus shellShell ID: 1 / Name: P74-26 capsid / Diameter: 824.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major head protein

MacromoleculeName: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Thermus virus P74-26
Molecular weightTheoretical: 46.680754 KDa
SequenceString: MRVPININNA LARVRDPLSI GGLKFPTTKE IQEAVAAIAD KFNQENDLVD RFFPEDSTFA SELELYLLRT QDAEQTGMTF VHQVGSTSL PVEARVAKVD LAKATWSPLA FKESRVWDEK EILYLGRLAD EVQAGVINEQ IAESLTWLMA RMRNRRRWLT W QVMRTGRI ...String:
MRVPININNA LARVRDPLSI GGLKFPTTKE IQEAVAAIAD KFNQENDLVD RFFPEDSTFA SELELYLLRT QDAEQTGMTF VHQVGSTSL PVEARVAKVD LAKATWSPLA FKESRVWDEK EILYLGRLAD EVQAGVINEQ IAESLTWLMA RMRNRRRWLT W QVMRTGRI TIQPNDPYNP NGLKYVIDYG VTDIELPLPQ KFDAKDGNGN SAVDPIQYFR DLIKAATYFP DRRPVAIIVG PG FDEVLAD NTFVQKYVEY EKGWVVGQNT VQPPREVYRQ AALDIFKRYT GLEVMVYDKT YRDQDGSVKY WIPVGELIVL NQS TGPVGR FVYTAHVAGQ RNGKVVYATG PYLTVKDHLQ DDPPYYAIIA GFHGLPQLSG YNTEDFSFHR FKWLKYANNV QSYL PPFPP KVEL

UniProtKB: Major head protein

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Macromolecule #2: P74-26 Head Decoration Protein

MacromoleculeName: P74-26 Head Decoration Protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Thermus virus P74-26
Molecular weightTheoretical: 16.37663 KDa
SequenceString:
MDKIQLFRTI GRVQYWERVP RLHAYGVFAL PFPMDPDVEW GNWFAGPHPK AFLVSVHPSG PKAGHVYPTD LSDPDSVANV IGMVLDGHD YEADHNVTVT LRAAVPIEYV QQGIEAPPLQ PDPAVLNAAP QLKLKVIKGH YFFDYTR

UniProtKB: Uncharacterized 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:
ConcentrationFormulaName
50.0 mMTris-HClTrisTris Hydrochloride Buffer
10.0 mMNaClSodium chlorideSodium Chloride
10.0 mMMgCl2Magnesium Chloride
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 45 second glow discharge, negative polarity, 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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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 / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 4611 / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio map generated with the dataset in cisTEM
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 3.7 degrees
Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationNumber classes: 4 / Software - Name: FREALIGN (ver. 9.11)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 3.7 degrees
Software - Name: FREALIGN (ver. 9.11)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 23174

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation Coefficient
Output model

PDB-6o3h:
Icosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid

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