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- EMDB-50521: Tail of emppty Haloferax tailed virus 1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50521
TitleTail of emppty Haloferax tailed virus 1
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: SPP1 gp17-like tail completion protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
  • Ligand: MAGNESIUM ION
KeywordsArcheal virus / portal / tail / VIRUS
Function / homologyHK97 gp6-like/SPP1 gp15-like head-tail connector / Tail tube protein / SPP1 gp17-like tail completion protein / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsZhang D / Daum B / Isupov MN / McLaren M
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
DepositionJun 3, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50521.png

Downloads & links

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Map

FileDownload / File: emd_50521.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 768 pix.
= 899.328 Å		1.17 Å/pix.
x 768 pix.
= 899.328 Å		1.17 Å/pix.
x 768 pix.
= 899.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0062
Minimum - Maximum-0.030950965 - 0.0727372
Average (Standard dev.)0.00012584006 (±0.0020537633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 899.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50521_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50521_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 : Haloferax tailed virus 1

EntireName: Haloferax tailed virus 1
Components
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: SPP1 gp17-like tail completion protein
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
  • Ligand: MAGNESIUM 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-#4 / 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 gp6-like/SPP1 gp15-like head-tail connector

MacromoleculeName: HK97 gp6-like/SPP1 gp15-like head-tail connector / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 15.585868 KDa
SequenceString:
MPDPSIDEVS KSDWDALTTQ EQDDIISQVE NLSSTGWVNT SRERKAEAIR SAIAERDTLY SGNMSRLPTL DGDAEYFTLY LSAHKIQLF EGGEAQSESG EGGSVSYSTG GGGEKDLQKT RYGRMALEYV WEDNSIAALR TY

UniProtKB: HK97 gp6-like/SPP1 gp15-like head-tail connector

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Macromolecule #2: SPP1 gp17-like tail completion protein

MacromoleculeName: SPP1 gp17-like tail completion protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 17.458789 KDa
SequenceString:
MATTSASHHV QAIIDLLEAA PDADWTPTQT PTVKRYWDDA QSERGPGADM PAILYVWSPT TSSLDRFSMD GDVFDQNDSI EVQAWSFDE TEVEQLQGDI VQILSEYLDD NEVQTPYSDV APTGTNDFRE QTPARTTGHY IMSVEVETRG LSETAKNA

UniProtKB: SPP1 gp17-like tail completion protein

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Macromolecule #3: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 3 / Number of copies: 66 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 17.177463 KDa
SequenceString:
MATSPEGIWS NSGALTFEDP ADDSEILFAG VRDVTITPAY EHAELYTIDS TFRDEVKRYE HNVNVEITYA KFSLEFAQEW LGGPGATAT ASQDDSDPMK FNLENVTPSA SGGFERTTAV ENVVFPELPL DSATYGEYEE YSLTGSGRSV TNLADTSGV

UniProtKB: Tail tube protein

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Macromolecule #4: Baseplate to tube adapter protein gp41

MacromoleculeName: Baseplate to tube adapter protein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 30.425914 KDa
SequenceString: MVDATLSRGG TSVDIPLVEE GGEILLSSTF GKPEVNVRKS GGSLNPRVID SWSGLQTFQL VGKLYDYSTS HQLADLVKTA STTPLELQI PQDAYPDTVT VAPAAGQASA LTLEYPAGRK DLVDVSLSLT RVDPNSVRGV GDQQATTPTT TGTGPVEVTA G GTTVQLPS ...String:
MVDATLSRGG TSVDIPLVEE GGEILLSSTF GKPEVNVRKS GGSLNPRVID SWSGLQTFQL VGKLYDYSTS HQLADLVKTA STTPLELQI PQDAYPDTVT VAPAAGQASA LTLEYPAGRK DLVDVSLSLT RVDPNSVRGV GDQQATTPTT TGTGPVEVTA G GTTVQLPS SGLSVERTVG RPNDAVRRVP RQADPRYEVK AKVTNDVFTF SFETLDNIPA TLNALTDNVF REQLGRDGVT LD FNGLLGL GSVKAIPVGS SPFRQVHQAG RGWVTVPTLE FRRIYSNE

UniProtKB: Uncharacterized protein

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 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 recording#0 - Image recording ID: 1 / #0 - Film or detector model: TFS FALCON 4i (4k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 54.6 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

Image recording ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6580
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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