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- EMDB-51915: The baseplate assembly of Haloferax tailed virus 1. -

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Basic information

Entry
Database: EMDB / ID: EMD-51915
TitleThe baseplate assembly of Haloferax tailed virus 1.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
    • Protein or peptide: Phate tail tape measure protein
  • Protein or peptide: Baseplate hub
  • Protein or peptide: Tail fiber protein gp42
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: ZINC ION
KeywordsArchaeal virus / tail / baseplate / tail fiber / VIRUS
Function / homologyBaseplate hub / Tail tube protein / Phate tail tape measure protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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: The baseplate assembly of Haloferax tailed virus 1.
Authors: Zhang D / Daum B / Isupov MN / McLaren M / Oksanen H / Quax TEF / Schwarzer S / Gold VAM / Stuart W
History
DepositionOct 28, 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_51915.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.171 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.025094314 - 0.06564252
Average (Standard dev.)-0.000048653455 (±0.002323419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 374.72 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: Tail tube protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
    • Protein or peptide: Phate tail tape measure protein
  • Protein or peptide: Baseplate hub
  • Protein or peptide: Tail fiber protein gp42
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: ZINC 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-#2, #5 / NCBI-ID: 2507575 / Sci species name: Haloferax tailed virus 1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloferax gibbonsii (archaea)

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Macromolecule #1: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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 #2: Baseplate to tube adapter protein gp41

MacromoleculeName: Baseplate to tube adapter protein gp41 / type: protein_or_peptide / ID: 2 / 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 #3: Baseplate hub

MacromoleculeName: Baseplate hub / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 102.541312 KDa
SequenceString: MPQLGDSKLG ESQLGSPGTL KQGVEWTVVV DGEEQNNVWD VQVVDTANPF GDYAVFKMDD RGGQAFEAYP RGTRVEAYVS EGTEPLDNR FTGYVVERRE NEQQGADVLE VEAYSFDQFL RRNTVTNDQT GNTISQALAD IIQTDTPVRF NAANITVGDD Q ELTRSYQG ...String:
MPQLGDSKLG ESQLGSPGTL KQGVEWTVVV DGEEQNNVWD VQVVDTANPF GDYAVFKMDD RGGQAFEAYP RGTRVEAYVS EGTEPLDNR FTGYVVERRE NEQQGADVLE VEAYSFDQFL RRNTVTNDQT GNTISQALAD IIQTDTPVRF NAANITVGDD Q ELTRSYQG DPVENALRDF AFKSTNEDFG VGDDLEFFFQ PRETVHIDRG VDNTQWFRYD IPELGKEAIN EVEVWFDDGE ES VIVDDGT DKLDLQDSLG LPSPGTQRKE LQRPLVTDIS DAEDIGRKYL AFRNSTLSGT VTTYGLYDAE PGDTIDITID PRG IDEEFV IAAIEYRWGV DETILTVVEK RGDVDDILSE LSESVQRIEM QGANRDAPKN RITTTNAAAI VSVDVDAGGT SADA DRFVN DGRNAVRDAW TGAGNPDIAN IVVGDDNSGL SRTNTTLGNQ TDSVSVTESL PSAKVVEYSA TLTQSGVEEI GLETS TGTL LTRATFETPV DLSSDTVTVT LTVSNDDSVS RGVMTNDGQT AVRDVLADNS PTLPTDYGYG DDSTAVAETD TTLGNE LAN TSLEEILIQS ASSVSAWNTI LGTLASTYPL VVSSSGIRPA QTAWTTESDN LAQSGTALVT VGDYSNGEAE GLDSPGD TL ELSFTPEHDI PGEEFALWCR IETDLGGTDP GPEITVTLDI DGDTYSWVPI GTNTALGLNW YDLANNTFGG SSTYPDTD I PEGSTVTLSI EATSSSVSGQ GHAVDVMAPL DALTRVTGGS DATSAYTFDN NNGGSGGYLD GPELYPDQLI LSLETATTR RNVSEARFTL TANDTSGNFY VELANDGSTF NRVNNATSGS VTFASPDTNV DTNISLNRYG SRSTATPQTG FNAQEIDNWE LYADIDAVL PDDIGVTLSR AIIPPNTSGI VGQTVREAGL KSGSTLLTRH ILAEFLLDTD QRLASSESTR FTSDN

UniProtKB: Baseplate hub

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Macromolecule #4: Tail fiber protein gp42

MacromoleculeName: Tail fiber protein gp42 / type: protein_or_peptide / ID: 4 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 29.020555 KDa
SequenceString: MADTTIIDAV VFPQDDGTGV SNGDEDYDSA GYLASLARYA GDGSYVGGDS TGSPTLQFAN IDTANEEVDI QPGHAFILES GHIVQSGSQ KTYDTNLPDS VPYVVILPSS VTNVPLDTDV DNDVWLAVDP TSNDSVYIRS GNGLSAPSDP SVKLGTVNSS T GSTTRPND ...String:
MADTTIIDAV VFPQDDGTGV SNGDEDYDSA GYLASLARYA GDGSYVGGDS TGSPTLQFAN IDTANEEVDI QPGHAFILES GHIVQSGSQ KTYDTNLPDS VPYVVILPSS VTNVPLDTDV DNDVWLAVDP TSNDSVYIRS GNGLSAPSDP SVKLGTVNSS T GSTTRPND LADHSVDALN ATTIDASDTV TGDTVDATTT LTDAAGVSHT GELEDINHGS KHEDGGSDEI SVGGLSGDLA DP QDPKAHA ASHSADSADE ISVENLSTTG SADTVPISQG DGTLSMGS

UniProtKB: Uncharacterized protein

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Macromolecule #5: Phate tail tape measure protein

MacromoleculeName: Phate tail tape measure protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 36.043656 KDa
SequenceString: MVAIRSEGVS ETQQNLEGVE NAMEDTADSA GDSAAELETF SKRFKGAMGA AVSALAIGTA GLLSQVPVVG EAMGGLGAII DALTMKIDE DARPAVGSFT DDLYEVAEAT YEADSSLEAF QTALDGVNTA IDDVAVSTLQ TEIEELTGIT IPKNWLDFGW D IMTLDARQ ...String:
MVAIRSEGVS ETQQNLEGVE NAMEDTADSA GDSAAELETF SKRFKGAMGA AVSALAIGTA GLLSQVPVVG EAMGGLGAII DALTMKIDE DARPAVGSFT DDLYEVAEAT YEADSSLEAF QTALDGVNTA IDDVAVSTLQ TEIEELTGIT IPKNWLDFGW D IMTLDARQ TMDNIETIIN EFPEDFGTML KSIDPRAKKG WDILTKSADM FINDLTSRID SGVNDVRGFF TGLASDLNEW GG NVASDAR EWGTNLIDKF TGGIRSKISG LRNWLSELRN IGAEVGIDVP TIGGGGDGGG GGGNSSRQPF AGGFFGGGNA TID GRQISE STGRYRSDPS RRRGI

UniProtKB: Phate tail tape measure protein

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 48 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 8 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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