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- EMDB-54133: Bacteriophage 812 prohead II with the complete set of minor capsi... -

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Basic information

Entry
Database: EMDB / ID: EMD-54133
TitleBacteriophage 812 prohead II with the complete set of minor capsid proteins
Map dataThe I4 reconstruction of the phage phi812 expanded procapsid was computed using RELION 5. This file is the masked output of the post-processing.
Sample
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Complex: The asymmetric unit of bacteriophage 812 prohead II with the complete set of minor capsid proteins
      • Protein or peptide: Putative Ig-like protein
      • Protein or peptide: Major capsid protein
      • Protein or peptide: Virion component
KeywordsBacterophage / phage cycle / capsid assembly / single particle analysis / the HK97 fold / Herelleviridae / VIRUS
Function / homology: / : / Major capsid protein
Function and homology information
Biological speciesStaphylococcus phage 812K1/420 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZlatohurska M / Prochazkova M / Cienikova Z / Fuzik T / Plevka P
Funding supportEuropean Union, Czech Republic, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)101043452European Union
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.01.01/00/22_008/0004607 Czech Republic
European Research Council (ERC)1233487European Union
CitationJournal: To Be Published
Title: Cryo-ET of S. aureus infection by Herelleviridae phage 812
Authors: Zlatohurska M / Prochazkova M / Cienikova Z / Fuzik T / Bardy P / Pantucek R / Plevka P
History
DepositionJun 23, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54133.png

Downloads & links

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Map

FileDownload / File: emd_54133.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe I4 reconstruction of the phage phi812 expanded procapsid was computed using RELION 5. This file is the masked output of the post-processing.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 1000 pix.
= 1283.52 Å		1.28 Å/pix.
x 1000 pix.
= 1283.52 Å		1.28 Å/pix.
x 1000 pix.
= 1283.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28352 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.042300083 - 0.07453652
Average (Standard dev.)0.00011953936 (±0.002649553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1283.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54133_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map was calculated in RELION with the...

Fileemd_54133_half_map_1.map
AnnotationHalf map was calculated in RELION with the Ewald sphere curvature correction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map was calculated in RELION with the...

Fileemd_54133_half_map_2.map
AnnotationHalf map was calculated in RELION with the Ewald sphere curvature correction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Staphylococcus phage 812K1/420

EntireName: Staphylococcus phage 812K1/420 (virus)
Components
  • Virus: Staphylococcus phage 812K1/420 (virus)
    • Complex: The asymmetric unit of bacteriophage 812 prohead II with the complete set of minor capsid proteins
      • Protein or peptide: Putative Ig-like protein
      • Protein or peptide: Major capsid protein
      • Protein or peptide: Virion component

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Supramolecule #1: Staphylococcus phage 812K1/420

SupramoleculeName: Staphylococcus phage 812K1/420 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Single particle analysis of capsid-like structures from the infected S. aureus cells
NCBI-ID: 3434241 / Sci species name: Staphylococcus phage 812K1/420 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Staphylococcus aureus (bacteria) / Strain: 1137
Virus shellShell ID: 1 / Name: capsid / Diameter: 1040.0 Å / T number (triangulation number): 16

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Supramolecule #2: The asymmetric unit of bacteriophage 812 prohead II with the comp...

SupramoleculeName: The asymmetric unit of bacteriophage 812 prohead II with the complete set of minor capsid proteins
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)

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Macromolecule #1: Putative Ig-like protein

MacromoleculeName: Putative Ig-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 19.624799 KDa
SequenceString:
AKKNVNDVLQ QESVTVADKY LQVKVNRDGY TRTHEGQYAY KVVSEGEELF LYPVQTDGKG TLNVMKKSPI AYTDGDNIHF VVNTVVDPY NHSFIRTEDI KGLDKGKQLI QAFLAFVEDR FKFGVYNVFV ANNKEDVLSI VDPTDNDADE VKDSLEHAHE D VIADFPAS PARKDV

UniProtKB: UNIPROTKB: A0A0U1UYD0

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Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 48.446559 KDa
SequenceString: SFQTGYGITP DTQIDAGALR REILDDQITM LTWTNEDLIF YRDISRRPAQ STVVKYDQYL RHGNVGHSRF VKEIGVAPVS DPNIRQKTV SMKYVSDTKN MSIASGLVNN IADPSQILTE DAIAVVAKTI EWASFYGDAS LTSEVEGEGL EFDGLAKLID K NNVINAKG ...String:
SFQTGYGITP DTQIDAGALR REILDDQITM LTWTNEDLIF YRDISRRPAQ STVVKYDQYL RHGNVGHSRF VKEIGVAPVS DPNIRQKTV SMKYVSDTKN MSIASGLVNN IADPSQILTE DAIAVVAKTI EWASFYGDAS LTSEVEGEGL EFDGLAKLID K NNVINAKG NQLTEKHLNE AAVRIGKGFG TATDAYMPIG VHADFVNSIL GRQMQLMQDN SGNVNTGYSV NGFYSSRGFI KL HGSTVME NELILDESLQ PLPNAPQPAK VTATVETKQK GAFENEEDRA GLSYKVVVNS DDAQSAPSEE VTATVSNVDD GVK LSINVN AMYQQQPQFV SIYRQGKETG MYFLIKRVPV KDAQEDGTIV FVDKNETLPE TADVFVGEMS PQVVHLFELL PMMK LPLAQ INASITFAVL WYGALALRAP KKWARIKNVR YIAV

UniProtKB: Major capsid protein

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Macromolecule #3: Virion component

MacromoleculeName: Virion component / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus phage 812K1/420 (virus)
Molecular weightTheoretical: 7.896915 KDa
SequenceString:
SKHIEITMSS GAKYFLVSTD EKSYNRQDID YMLRGMDETS IKVYTESAIT SPQVYINPNR IESFKIVF

UniProtKB: UNIPROTKB: A0A0U1WYT8

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMNaClsodium chloride
10.0 mMCaCl2calcium chloride
50.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride

Details: Phage buffer, adjusted by Tris-HCl (pH 8) to a final pH of approx. 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 110 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 4.7000000000000004e-05 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV / Details: One-side blotting.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 21755 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 68779
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

8304

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0beta) / Number images used: 20569
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0beta)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 5.0beta)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5lii


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9rox:
Asymmetric unit of bacteriophage 812 prohead II with the complete set of minor capsid proteins

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