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- PDB-9i8c: GBSV1 portal protein without the N-terminal tail -

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Basic information

Entry
Database: PDB / ID: 9i8c
TitleGBSV1 portal protein without the N-terminal tail
ComponentsPhage portal protein
KeywordsVIRAL PROTEIN / GBSV1 / Portal protein / Geobacillus phage GSBV1
Function / homologyPhage portal protein, HK97 / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage portal protein
Function and homology information
Biological speciesGeobacillus phage GBSV1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChong, P.J. / Chechik, M. / Jenkins, H. / Greive, S. / Antson, F.
Funding support United Kingdom, France, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Other private France
CitationJournal: To Be Published
Title: GBSV1 portal protein without the N-terminal tail
Authors: Chong, P.J. / Chechik, M. / Jenkins, H. / Greive, S. / Antson, F.
History
DepositionFeb 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage portal protein


Theoretical massNumber of molelcules
Total (without water)38,2731
Polymers38,2731
Non-polymers00
Water00
1
A: Phage portal protein
x 12


Theoretical massNumber of molelcules
Total (without water)459,27412
Polymers459,27412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11

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Components

#1: Protein Phage portal protein


Mass: 38272.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus phage GBSV1 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q0H263
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: GBSV1 portal protein / Type: COMPLEX
Details: The N-terminal tail (M1-V40) was removed during cloning. The C-terminal end (E379-D406) could not be modelled, so has been omitted from the coordinate file.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Geobacillus phage GBSV1 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris-HCL1
20.25 MSodium chlorideNaCl1
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Blot time 1s, force -10, wait time 5s

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 240000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingAverage exposure time: 4.81 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.9.8.5model fitting
9PHENIX1.21.1_5286model refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 973630
SymmetryPoint symmetry: C12 (12 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21727 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038247
ELECTRON MICROSCOPYf_angle_d0.62111178
ELECTRON MICROSCOPYf_dihedral_angle_d4.9591116
ELECTRON MICROSCOPYf_chiral_restr0.0411254
ELECTRON MICROSCOPYf_plane_restr0.0051440

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