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- PDB-7sz4: Kinetically trapped Pseudomonas-phage PaP3 portal protein - delta... -

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Basic information

Entry
Database: PDB / ID: 7sz4
TitleKinetically trapped Pseudomonas-phage PaP3 portal protein - delta barrel mutant class-2
ComponentsPortal protein
KeywordsVIRAL PROTEIN / Portal protein / Dodecamer
Function / homology: / Phage SU10 portal protein / ORF.04
Function and homology information
Biological speciesPseudomonas virus PaP3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsHou, C.-F.D. / Swanson, N.A. / Li, F. / Yang, R. / Lokareddy, R.K. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 GM100888, R35 GM140733-0, P30 CA56036, HSSN261200800001E United States
CitationJournal: J Mol Biol / Year: 2022
Title: Cryo-EM Structure of a Kinetically Trapped Dodecameric Portal Protein from the Pseudomonas-phage PaP3.
Authors: Chun-Feng David Hou / Nicholas A Swanson / Fenglin Li / Ruoyu Yang / Ravi K Lokareddy / Gino Cingolani /
Abstract: Portal proteins are dodecameric assemblies that occupy a unique 5-fold vertex of the icosahedral capsid of tailed bacteriophages and herpesviruses. The portal vertex interrupts the icosahedral ...Portal proteins are dodecameric assemblies that occupy a unique 5-fold vertex of the icosahedral capsid of tailed bacteriophages and herpesviruses. The portal vertex interrupts the icosahedral symmetry, and in vivo, its assembly and incorporation in procapsid are controlled by the scaffolding protein. Ectopically expressed portal oligomers are polymorphic in solution, and portal rings built by a different number of subunits have been documented in the literature. In this paper, we describe the cryo-EM structure of the portal protein from the Pseudomonas-phage PaP3, which we determined at 3.4 Å resolution. Structural analysis revealed a dodecamer with helical rather than rotational symmetry, which we hypothesize is kinetically trapped. The helical assembly was stabilized by local mispairing of portal subunits caused by the slippage of crown and barrel helices that move like a lever with respect to the portal body. Removing the C-terminal barrel promoted assembly of undecameric and dodecameric rings with quasi-rotational symmetry, suggesting that the barrel contributes to subunits mispairing. However, ΔC-portal rings were intrinsically asymmetric, with most particles having one open portal subunit interface. Together, these data expand the structural repertoire of viral portal proteins to Pseudomonas-phages and shed light on the unexpected plasticity of the portal protein quaternary structure.
History
DepositionNov 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Mar 30, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0Mar 30, 2022Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 30, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
k: Portal protein
j: Portal protein
i: Portal protein
h: Portal protein
l: Portal protein
a: Portal protein
b: Portal protein
c: Portal protein
d: Portal protein
e: Portal protein
f: Portal protein
g: Portal protein


Theoretical massNumber of molelcules
Total (without water)971,77612
Polymers971,77612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein


Mass: 80981.344 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas virus PaP3 / Gene: orf4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H9R8
Has protein modificationN

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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: Dodecameric complex of phage PaP3 portal, C-terminal truncated mutant
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Phage PaP3 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl1
2200 mMNaCl1
35 mMEDTA1
SpecimenConc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1.2particle selection
4CTFFIND4CTF correction
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1200000
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74000 / Symmetry type: POINT
Atomic model buildingB value: 129 / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00349064
ELECTRON MICROSCOPYf_angle_d0.75766173
ELECTRON MICROSCOPYf_dihedral_angle_d5.5656541
ELECTRON MICROSCOPYf_chiral_restr0.0467239
ELECTRON MICROSCOPYf_plane_restr0.0058652

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