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- PDB-9h7v: The baseplate assembly of Haloferax tailed virus 1. -

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Basic information

Entry
Database: PDB / ID: 9h7v
TitleThe baseplate assembly of Haloferax tailed virus 1.
Components
  • Baseplate hub
  • Baseplate to tube adapter protein gp41
  • Phate tail tape measure protein
  • Tail fiber protein gp42
  • Tail tube protein
KeywordsVIRUS / Archaeal virus / tail / baseplate / tail fiber
Function / homology: / Baseplate hub / Tail tube protein / Phate tail tape measure protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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: The baseplate assembly of Haloferax tailed virus 1.
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 28, 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
B1: Tail tube protein
B2: Tail tube protein
B3: Tail tube protein
B4: Tail tube protein
B5: Tail tube protein
B6: Tail tube protein
BA: Baseplate to tube adapter protein gp41
BB: Baseplate to tube adapter protein gp41
BC: Baseplate to tube adapter protein gp41
BD: Baseplate hub
BE: Baseplate hub
BF: Baseplate hub
BG: Tail fiber protein gp42
BH: Tail fiber protein gp42
BI: Tail fiber protein gp42
BJ: Tail fiber protein gp42
BK: Tail fiber protein gp42
BL: Tail fiber protein gp42
BM: Tail fiber protein gp42
BN: Tail fiber protein gp42
BO: Tail fiber protein gp42
QE: Phate tail tape measure protein
QF: Phate tail tape measure protein
QG: Phate tail tape measure protein
QH: Phate tail tape measure protein
QI: Phate tail tape measure protein
QJ: Phate tail tape measure protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)981,28589
Polymers979,41327
Non-polymers1,87262
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 , 5 types, 27 molecules B1B2B3B4B5B6BABBBCBDBEBFBGBHBIBJBKBLBMBNBOQEQFQGQHQIQJ

#1: Protein
Tail tube protein


Mass: 17177.463 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6U0
#2: 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
#3: 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
#4: Protein
Tail fiber protein gp42


Mass: 29020.555 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N721
#5: 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

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Non-polymers , 3 types, 62 molecules

#6: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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-#2, #5 / Source: NATURAL
Source (natural)Organism: Haloferax tailed virus 1
Details of virusEmpty: NO / 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 recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135152 / Symmetry type: POINT

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