[English] 日本語
Yorodumi
- EMDB-51866: Tail of full Haloferax tailed virus 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51866
TitleTail of full Haloferax tailed virus 1
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Baseplate hub
    • Protein or peptide: Phate tail tape measure protein
    • Protein or peptide: Baseplate to tube adapter protein gp41
    • Protein or peptide: Tail tube protein
    • Protein or peptide: SPP1 gp17-like tail completion protein
    • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: Portal protein
  • Ligand: MAGNESIUM ION
KeywordsArchaeal virus / portal / tail / baseplate / tape measure protein / VIRUS
Function / homologyPortal protein / HK97 gp6-like/SPP1 gp15-like head-tail connector / Baseplate hub / Tail tube protein / SPP1 gp17-like tail completion protein / Phate tail tape measure protein / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 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 / Stuart W
History
DepositionOct 21, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_51866.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.171 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0253447 - 0.07305847
Average (Standard dev.)0.00027756437 (±0.0018455108)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : Haloferax tailed virus 1

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

-
Supramolecule #1: Haloferax tailed virus 1

SupramoleculeName: Haloferax tailed virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / 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)

-
Macromolecule #1: Baseplate hub

MacromoleculeName: Baseplate hub / type: protein_or_peptide / ID: 1 / 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

-
Macromolecule #2: Phate tail tape measure protein

MacromoleculeName: Phate tail tape measure protein / type: protein_or_peptide / ID: 2 / 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

-
Macromolecule #3: Baseplate to tube adapter protein gp41

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

-
Macromolecule #4: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 4 / 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

-
Macromolecule #5: SPP1 gp17-like tail completion protein

MacromoleculeName: SPP1 gp17-like tail completion protein / type: protein_or_peptide / ID: 5 / 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

-
Macromolecule #6: HK97 gp6-like/SPP1 gp15-like head-tail connector

MacromoleculeName: HK97 gp6-like/SPP1 gp15-like head-tail connector / type: protein_or_peptide / ID: 6 / 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

-
Macromolecule #7: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 7 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 75.680906 KDa
SequenceString: MPKYNLRIGN RRVPIASTDT PLSEAIGKRL ASSTPQTNVD SMGGGHSYQF NGQDLTFEDL RDIKDVRDSG GQVAQLMDYK ALLNFGEGC EIHVEGDDET KQLVDGEPMT LSEWLEDAFP HLDLLVLDLG GDALWYPYAV GEIQETITGE FKEALPAEPW T LMPESDAQ ...String:
MPKYNLRIGN RRVPIASTDT PLSEAIGKRL ASSTPQTNVD SMGGGHSYQF NGQDLTFEDL RDIKDVRDSG GQVAQLMDYK ALLNFGEGC EIHVEGDDET KQLVDGEPMT LSEWLEDAFP HLDLLVLDLG GDALWYPYAV GEIQETITGE FKEALPAEPW T LMPESDAQ GKVQAWHQRT KTHGGYQTQT LPADDLW(HIP)IV INKASARDEV GISEVLRNKD EIQAFKQNEA AINQAIEL H GFPQR(HIP)VKVG KEDGAPVRDN DLRRVRTIFD PRTTDANTAY FTGQDVDVET LEA(HIP)NFDYSA IHEMDMRNLT T ALGLPLEA GNVGADGLGS GKPAELRFAL LKLAIKANQR SFSVQFVERV MRPVVRDYSP FDHEADIRLE INDPLEDIGE VA DLIQQVG DYMTNEQVAE KLDLPAPEDD EVADSYRSPA DMEKDEAGVQ DEPFGGMFAG RDMGNRCLGE GITDDELQHA PEW DRPLLE MYQGVTNPES DTSRTLVSFS SSGTPEFVLE RIRESIMDGA LFSEFDNIPS SRLMELRQTF ADELGTDNFT LDSI TDALM DFEADLTRDA AERIARTESS AVLNHAREIS YEERGEGNEL FYWTGADLGD SRQTEACAWL IRQTNPFSGG TPVPM NELR DMVDEAPSHD DSMDNNLARP DSWVVHPNER SSFVKAPPNW EQL

UniProtKB: Portal protein

-
Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 15 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Image recording ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116880
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more