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- PDB-9h4p: Tail of full Haloferax tailed virus 1 -

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Basic information

Entry
Database: PDB / ID: 9h4p
TitleTail of full Haloferax tailed virus 1
Components
  • Baseplate hub
  • Baseplate to tube adapter protein gp41
  • HK97 gp6-like/SPP1 gp15-like head-tail connector
  • Phate tail tape measure protein
  • Portal protein
  • SPP1 gp17-like tail completion protein
  • Tail tube protein
KeywordsVIRUS / Archaeal virus / portal / tail / baseplate / tape measure protein
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsZhang, D. / Daum, B. / Isupov, M.N. / McLaren, M.
Funding supportEuropean Union, 1items
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, M.N. / McLaren, M. / Oksanen, H. / Quax, T.E.F. / Schwarzer, S. / Gold, V.A.M. / Stuart, W.
History
DepositionOct 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BD: Baseplate hub
BE: Baseplate hub
BF: Baseplate hub
QG: Phate tail tape measure protein
QH: Phate tail tape measure protein
QI: Phate tail tape measure protein
QJ: Phate tail tape measure protein
QE: Phate tail tape measure protein
QF: Phate tail tape measure protein
BA: Baseplate to tube adapter protein gp41
BB: Baseplate to tube adapter protein gp41
BC: Baseplate to tube adapter protein gp41
SG: Tail tube protein
SH: Tail tube protein
SI: Tail tube protein
SJ: Tail tube protein
SK: Tail tube protein
SL: Tail tube protein
SS: Tail tube protein
ST: Tail tube protein
SU: Tail tube protein
SV: Tail tube protein
SW: Tail tube protein
SX: Tail tube protein
SM: Tail tube protein
SN: Tail tube protein
SO: Tail tube protein
SP: Tail tube protein
SQ: Tail tube protein
SR: Tail tube protein
SB: Tail tube protein
SA: Tail tube protein
SC: Tail tube protein
SD: Tail tube protein
SE: Tail tube protein
SF: Tail tube protein
Sk: Tail tube protein
Sl: Tail tube protein
Sm: Tail tube protein
Sn: Tail tube protein
So: Tail tube protein
Sp: Tail tube protein
Se: Tail tube protein
Sf: Tail tube protein
Sg: Tail tube protein
Sh: Tail tube protein
Si: Tail tube protein
Sj: Tail tube protein
SY: Tail tube protein
SZ: Tail tube protein
Sa: Tail tube protein
Sb: Tail tube protein
Sc: Tail tube protein
Sd: Tail tube protein
B1: Tail tube protein
B2: Tail tube protein
B3: Tail tube protein
B4: Tail tube protein
B5: Tail tube protein
B6: Tail tube protein
Sw: Tail tube protein
Sx: Tail tube protein
Sy: Tail tube protein
Sz: Tail tube protein
S1: Tail tube protein
S2: Tail tube protein
Sq: Tail tube protein
Sr: Tail tube protein
Ss: Tail tube protein
St: Tail tube protein
Su: Tail tube protein
Sv: Tail tube protein
P1: Tail tube protein
P2: Tail tube protein
P3: Tail tube protein
P4: Tail tube protein
P5: Tail tube protein
P6: Tail tube protein
Pa: SPP1 gp17-like tail completion protein
Pb: SPP1 gp17-like tail completion protein
Pc: SPP1 gp17-like tail completion protein
Pd: SPP1 gp17-like tail completion protein
Pe: SPP1 gp17-like tail completion protein
Pf: SPP1 gp17-like tail completion protein
PT: HK97 gp6-like/SPP1 gp15-like head-tail connector
PM: HK97 gp6-like/SPP1 gp15-like head-tail connector
PN: HK97 gp6-like/SPP1 gp15-like head-tail connector
PO: HK97 gp6-like/SPP1 gp15-like head-tail connector
PP: HK97 gp6-like/SPP1 gp15-like head-tail connector
PQ: HK97 gp6-like/SPP1 gp15-like head-tail connector
PR: HK97 gp6-like/SPP1 gp15-like head-tail connector
PS: HK97 gp6-like/SPP1 gp15-like head-tail connector
PU: HK97 gp6-like/SPP1 gp15-like head-tail connector
PV: HK97 gp6-like/SPP1 gp15-like head-tail connector
PW: HK97 gp6-like/SPP1 gp15-like head-tail connector
PX: HK97 gp6-like/SPP1 gp15-like head-tail connector
PA: Portal protein
PB: Portal protein
PC: Portal protein
PD: Portal protein
PE: Portal protein
PF: Portal protein
PG: Portal protein
PH: Portal protein
PI: Portal protein
PJ: Portal protein
PK: Portal protein
PL: Portal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,949,195123
Polymers2,948,830108
Non-polymers36515
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 108 molecules BDBEBFQGQHQIQJQEQFBABBBCSGSHSISJSKSLSSSTSUSVSWSXSMSNSOSPSQSR...

#1: Protein Baseplate hub


Mass: 102541.312 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6T6
#2: Protein
Phate tail tape measure protein


Mass: 36043.656 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6W4
#3: Protein Baseplate to tube adapter protein gp41


Mass: 30425.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6X8
#4: Protein ...
Tail tube protein


Mass: 17177.463 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6U0
#5: Protein
SPP1 gp17-like tail completion protein


Mass: 17458.789 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6U9
#6: Protein
HK97 gp6-like/SPP1 gp15-like head-tail connector


Mass: 15585.868 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6S3
#7: Protein
Portal protein


Mass: 75680.906 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6Q2

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Non-polymers , 1 types, 15 molecules

#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Haloferax tailed virus 1 / Type: VIRUS / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Haloferax tailed virus 1
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Haloferax gibbonsii
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150TFS FALCON 4i (4k x 4k)
2154.6GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2REFMAC5.8.0267model refinement
3EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116880 / Symmetry type: POINT

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