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

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Basic information

Entry
Database: PDB / ID: 6o3h
TitleIcosahedral reconstruction of the thermophilic bacteriophage P74-26 capsid
Components
  • Major head protein
  • 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsStone, N.P. / Demo, G. / Agnello, E. / Kelch, B.A.
Funding support United States, 1items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: P74-26 Head Decoration Protein
I: P74-26 Head Decoration Protein
J: P74-26 Head Decoration Protein
K: P74-26 Head Decoration Protein
L: P74-26 Head Decoration Protein
M: P74-26 Head Decoration Protein
N: P74-26 Head Decoration Protein


Theoretical massNumber of molelcules
Total (without water)441,40214
Polymers441,40214
Non-polymers00
Water0
1
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: P74-26 Head Decoration Protein
I: P74-26 Head Decoration Protein
J: P74-26 Head Decoration Protein
K: P74-26 Head Decoration Protein
L: P74-26 Head Decoration Protein
M: P74-26 Head Decoration Protein
N: P74-26 Head Decoration Protein
x 60


Theoretical massNumber of molelcules
Total (without water)26,484,101840
Polymers26,484,101840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: P74-26 Head Decoration Protein
I: P74-26 Head Decoration Protein
J: P74-26 Head Decoration Protein
K: P74-26 Head Decoration Protein
L: P74-26 Head Decoration Protein
M: P74-26 Head Decoration Protein
N: P74-26 Head Decoration Protein
x 5


  • icosahedral pentamer
  • 2.21 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)2,207,00870
Polymers2,207,00870
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: P74-26 Head Decoration Protein
I: P74-26 Head Decoration Protein
J: P74-26 Head Decoration Protein
K: P74-26 Head Decoration Protein
L: P74-26 Head Decoration Protein
M: P74-26 Head Decoration Protein
N: P74-26 Head Decoration Protein
x 6


  • icosahedral 23 hexamer
  • 2.65 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,648,41084
Polymers2,648,41084
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major head protein


Mass: 46680.754 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Thermus virus P74-26 / References: UniProt: A7XXR6
#2: Protein
P74-26 Head Decoration Protein


Mass: 16376.630 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Thermus virus P74-26 / References: UniProt: A7XXR5

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Thermus phage P7426 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermus phage P7426 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Thermus thermophilus / Strain: HB8
Virus shellName: P74-26 capsid / Diameter: 824 nm / Triangulation number (T number): 7
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris Hydrochloride BufferTris-HClTris1
210 mMSodium ChlorideNaClSodium chloride1
310 mMMagnesium ChlorideMgCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 45 second glow discharge, negative polarity, 20 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4611

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Processing

EM software
IDNameVersionCategory
1cisTEM1particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Coot0.8model fitting
9FREALIGN9.11initial Euler assignment
10FREALIGN9.11final Euler assignment
11FREALIGN9.11classification
12FREALIGN9.113D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23174 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation Coefficient

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