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- EMDB-51530: Capsid of full Haloferax tailed virus 1 without turret head prote... -

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Basic information

Entry
Database: EMDB / ID: EMD-51530
TitleCapsid of full Haloferax tailed virus 1 without turret head protein gp31.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp5-like major capsid protein
    • Protein or peptide: Capsid stabilization protein
    • Protein or peptide: Gp30
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsArchaeal virus / turret / capsid / VIRUS
Function / homologyCapsid stabilization protein / HK97 gp5-like major capsid protein / Gp30
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZhang D / Daum B / Isupov MN / McLaren M / Stuart W
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: CryoEM structure of Haloferax tailed virus
Authors: Zhang D / Daum B / Isupov MN / McLaren M / Oksanen H / Quax TEF / Schwarzer S / Gold VAM
History
DepositionSep 13, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_51530.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.171 Å
Density
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.1294665 - 2.5792527
Average (Standard dev.)0.016027447 (±0.13655081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions896896896
Spacing896896896
CellA=B=C: 1049.2161 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Haloferax tailed virus 1

EntireName: Haloferax tailed virus 1
Components
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp5-like major capsid protein
    • Protein or peptide: Capsid stabilization protein
    • Protein or peptide: Gp30
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: Haloferax tailed virus 1

SupramoleculeName: Haloferax tailed virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 2507575 / Sci species name: Haloferax tailed virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Haloferax gibbonsii (archaea)

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Macromolecule #1: HK97 gp5-like major capsid protein

MacromoleculeName: HK97 gp5-like major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 43.544406 KDa
SequenceString: MLMEAALPGS DVSAREVAKV WPGAKKGDYS FLQGNQSRSL EAEMTRTARA EAGTDRHRAL KDYAVDADNL PKTLSAGSKH LTEDGDVIE ARLDDAIPRM LFAASDPEYV DTLFREQLLE VVMEGRELRK VAREASNVIN ANTRVGDVPI ASDEEFARPT G QGAEIRDD ...String:
MLMEAALPGS DVSAREVAKV WPGAKKGDYS FLQGNQSRSL EAEMTRTARA EAGTDRHRAL KDYAVDADNL PKTLSAGSKH LTEDGDVIE ARLDDAIPRM LFAASDPEYV DTLFREQLLE VVMEGRELRK VAREASNVIN ANTRVGDVPI ASDEEFARPT G QGAEIRDD GETYTTVAWN ATKLTEGSRV TDEMRDQAMV DLIERNIQRV GASLENGINR VFLTELVDNA QNNHDTAGSN QG YQALNSA VGEVDKDDFR PDTYVTHPDY RTQLFNDTNL AYANRAGTNE VLRNREDAPI VGDIAGLDMH AAMSSATYDD GTD IGWSGG SETWGFSSDG DKGAVVYDRD NIHTILYAPN GQDVEIKDYE DPIRDITGVN GRLHVDCQYS QGRSSATVQY

UniProtKB: HK97 gp5-like major capsid protein

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Macromolecule #2: Capsid stabilization protein

MacromoleculeName: Capsid stabilization protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 13.888911 KDa
SequenceString:
MATETQGEHT FPVEVLISGE ELRGYTAGEA LSAGEPVYLS GDYEVSASSA DGGEFLGVNL YDVASGEPVA LAGDDCEVRV EVSEQVTAN DEILPDGLGT FETVATSAAS AGVAIVQEGA ASGEVCEAYI FAVQGTTA

UniProtKB: Capsid stabilization protein

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Macromolecule #3: Gp30

MacromoleculeName: Gp30 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 11.92676 KDa
SequenceString:
MTDTIVNVQG SFFSASASGV ADTESLLIDP QDAKFGAIEI HNIAHGGSVD VELLTSSDDT ELVEDAAVTL DSFTGEGISQ GNQIEASDN TNTYIRITNT SGGAIDIIAT GREVSQ

UniProtKB: Gp30

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 48 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2512500
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-9gs0:
Capsid of full Haloferax tailed virus 1 without turret head protein gp31.

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