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- PDB-5l35: Cryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5l35
TitleCryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution
ComponentsGene 5 protein
KeywordsVIRUS / phage / Sf6
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / Gene 5 protein
Function and homology information
Biological speciesShigella phage Sf6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhao, H. / Tang, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090010 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy.
Authors: Haiyan Zhao / Kunpeng Li / Anna Y Lynn / Keith E Aron / Guimei Yu / Wen Jiang / Liang Tang /
Abstract: The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand ...The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Mar 6, 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
  • EMDB-8314
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Gene 5 protein
B: Gene 5 protein
C: Gene 5 protein
D: Gene 5 protein
E: Gene 5 protein
F: Gene 5 protein
G: Gene 5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,1718
Polymers319,1367
Non-polymers351
Water00
1
A: Gene 5 protein
B: Gene 5 protein
C: Gene 5 protein
D: Gene 5 protein
E: Gene 5 protein
F: Gene 5 protein
G: Gene 5 protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)19,150,280480
Polymers19,148,153420
Non-polymers2,12760
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: Gene 5 protein
B: Gene 5 protein
C: Gene 5 protein
D: Gene 5 protein
E: Gene 5 protein
F: Gene 5 protein
G: Gene 5 protein
hetero molecules
x 5


  • icosahedral pentamer
  • 1.6 MDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)1,595,85740
Polymers1,595,67935
Non-polymers1775
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Gene 5 protein
B: Gene 5 protein
C: Gene 5 protein
D: Gene 5 protein
E: Gene 5 protein
F: Gene 5 protein
G: Gene 5 protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.92 MDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)1,915,02848
Polymers1,914,81542
Non-polymers2136
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
Gene 5 protein


Mass: 45590.840 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716H0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: Shigella phage Sf6 / Type: VIRUS / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 19.5 MDa / Experimental value: NO
Source (natural)Organism: Shigella phage Sf6 (virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Shigella flexneri / Strain: M94
Virus shellName: virus capsid / Diameter: 650 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110.0 mMTrisC4H11NO31
21.0 mMmagnesium chlorideMgCl21
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: purified Sf6 phage
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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 FIELD
Image recordingElectron dose: 9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND3CTF correction
7PHENIX1.1model fitting
8Coot8.2model fitting
11jspr1final Euler assignment
13jspr13D reconstruction
14PHENIX1.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68000 / Symmetry type: POINT
Atomic model buildingB value: 46.6 / Protocol: AB INITIO MODEL / Space: RECIPROCAL
Target criteria: Pseudo-crystallographic R factor and stereochemistry

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