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- PDB-7z4w: gp6/gp15/gp16 connector complex of bacteriophage SPP1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7z4w
Titlegp6/gp15/gp16 connector complex of bacteriophage SPP1
Components
  • Head completion protein gp15
  • Head completion protein gp16
  • Portal protein
KeywordsVIRAL PROTEIN / Bacteriophage / SPP1 / Portal Protein / Head completion proteins / Connector Complex / DNA Channel
Function / homology
Function and homology information


viral DNA genome packaging, headful / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / viral procapsid / virion component
Similarity search - Function
Portal protein, SPP1-type / Portal protein / : / Phage portal protein, SPP1 Gp6-like / Phage gp6-like head-tail connector protein / Phage gp6-like head-tail connector protein / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily
Similarity search - Domain/homology
Head completion protein gp16 / Portal protein / Head completion protein gp15
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsOrlov, I. / Roche, S. / Tavares, P. / Orlova, E.V.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)CNRS funding France
CitationJournal: Nat Commun / Year: 2022
Title: CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper.
Authors: Igor Orlov / Stéphane Roche / Sandrine Brasilès / Natalya Lukoyanova / Marie-Christine Vaney / Paulo Tavares / Elena V Orlova /
Abstract: Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 ...Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp6gp15gp16) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage.
History
DepositionMar 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Portal protein
B: Portal protein
a: Head completion protein gp15
b: Head completion protein gp15
1: Head completion protein gp16
C: Portal protein
D: Portal protein
c: Head completion protein gp15
d: Head completion protein gp15
2: Head completion protein gp16
E: Portal protein
F: Portal protein
e: Head completion protein gp15
f: Head completion protein gp15
3: Head completion protein gp16
G: Portal protein
H: Portal protein
g: Head completion protein gp15
h: Head completion protein gp15
4: Head completion protein gp16
I: Portal protein
J: Portal protein
i: Head completion protein gp15
j: Head completion protein gp15
5: Head completion protein gp16
K: Portal protein
L: Portal protein
k: Head completion protein gp15
l: Head completion protein gp15
6: Head completion protein gp16


Theoretical massNumber of molelcules
Total (without water)903,56630
Polymers903,56630
Non-polymers00
Water7,314406
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein / Gene product 6 / gp6 / Portal vertex protein


Mass: 57390.277 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P54309
#2: Protein
Head completion protein gp15 / HCP / Connector protein gp15 / Gene product 15 / Gp15


Mass: 11629.402 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: Q38584
#3: Protein
Head completion protein gp16 / Connector protein gp16 / Gene product 16 / Gp16 / Stopper protein gp16


Mass: 12554.990 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: O48446
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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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: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 0.902 kDa/nm / Experimental value: NO
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: YB886
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl pH 7.51
250 mMSodium ChlorideNaClSodium chloride1
35 mMMagnesium ChlorideMgCl21
SpecimenConc.: 0.64 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 96 % / Chamber temperature: 277 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: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3876

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot9model fitting
9cryoSPARC2initial Euler assignment
10cryoSPARC2final Euler assignment
11cryoSPARC2classification
12cryoSPARC23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 520000
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 401807
Details: Local resolution variations in the reconstruction was estimated using ResMap
Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: FLEXIBLE FIT / Space: REAL
Details: Manual inspection of the residues in the complete gp6, gp15 and gp16 polypeptide chains tracing was done using COOT and refined in Phenix
Atomic model building
IDPDB-ID 3D fitting-IDPdb chain residue range
12JES

2jes

1254-344
21
31

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