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- EMDB-52713: GBSV1 portal protein without the N-terminal tail -

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Basic information

Entry
Database: EMDB / ID: EMD-52713
TitleGBSV1 portal protein without the N-terminal tail
Map data
Sample
  • Complex: GBSV1 portal protein
    • Protein or peptide: Phage portal protein
KeywordsGBSV1 / Portal protein / Geobacillus phage GSBV1 / VIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChong PJ / Chechik M / Jenkins H / Greive S / Antson F
Funding support United Kingdom, France, 2 items
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 PJ / Chechik M / Jenkins H / Greive S / Antson F
History
DepositionFeb 4, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52713.png

Downloads & links

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Map

FileDownload / File: emd_52713.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 257.152 Å		1 Å/pix.
x 256 pix.
= 257.152 Å		1 Å/pix.
x 256 pix.
= 257.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.052286025 - 0.09395789
Average (Standard dev.)0.00019669706 (±0.004711101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 257.152 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52713_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52713_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52713_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GBSV1 portal protein

EntireName: GBSV1 portal protein
Components
  • Complex: GBSV1 portal protein
    • Protein or peptide: Phage portal protein

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Supramolecule #1: GBSV1 portal protein

SupramoleculeName: GBSV1 portal protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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.
Source (natural)Organism: Geobacillus phage GBSV1 (virus)

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Macromolecule #1: Phage portal protein

MacromoleculeName: Phage portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus phage GBSV1 (virus)
Molecular weightTheoretical: 38.272805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RLSDNPEVRM AVHKIADLIS SMTIYLMQNT EDGDIRIRNE LSRKIDITPY SLMTRKSWMY NIVYTMLLDG EGNSVVFPKY TADGLIDEL VPLTPSKVNF LDTPDGYQVL YGGQTFNYDE VLHFIYNPDP ERPYIGRGYR VVLKDIADNL KQATATKKSF M SGKYMPSL ...String:
RLSDNPEVRM AVHKIADLIS SMTIYLMQNT EDGDIRIRNE LSRKIDITPY SLMTRKSWMY NIVYTMLLDG EGNSVVFPKY TADGLIDEL VPLTPSKVNF LDTPDGYQVL YGGQTFNYDE VLHFIYNPDP ERPYIGRGYR VVLKDIADNL KQATATKKSF M SGKYMPSL IVKVDAATAE LSSEEGRNAV FKKYLQATEA GQPWIIPAEL LEVEQVKPLS LKDIAINEAV ELDKRTVAGM FG VPAFLLG IGEFNRDEYN NFINSTILPI AKGIEQELTR KLLISPDLYF KFNPRSLYAY DLKELAEVGS NMYVRGIMEG NEV RDWLGL SPKEGLSELV IL

UniProtKB: Phage portal protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HCLTris
0.25 MNaClSodium chloride
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 1s, force -10, wait time 5s.

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Electron microscopy

MicroscopeTFS GLACIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average exposure time: 4.81 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 240000

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Image processing

Particle selectionNumber selected: 973630
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 21727
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 4)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot (ver. 0.9.8.5)
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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