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- PDB-9gs0: Capsid of full Haloferax tailed virus 1 without turret head prote... -

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Basic information

Entry
Database: PDB / ID: 9gs0
TitleCapsid of full Haloferax tailed virus 1 without turret head protein gp31.
Components
  • Capsid stabilization protein
  • Gp30
  • HK97 gp5-like major capsid protein
KeywordsVIRUS / Archaeal virus / turret / capsid
Function / homology: / Capsid stabilization protein / HK97 gp5-like major capsid protein / Gp30
Function and homology information
Biological speciesHaloferax tailed virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsZhang, D. / Daum, B. / Isupov, M.N. / McLaren, M. / Stuart, W.
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.
History
DepositionSep 13, 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
AA: HK97 gp5-like major capsid protein
AB: HK97 gp5-like major capsid protein
AC: HK97 gp5-like major capsid protein
AD: HK97 gp5-like major capsid protein
AE: HK97 gp5-like major capsid protein
AF: HK97 gp5-like major capsid protein
AI: Capsid stabilization protein
AJ: Capsid stabilization protein
AK: Capsid stabilization protein
AL: Capsid stabilization protein
AM: Capsid stabilization protein
AN: Capsid stabilization protein
AO: Capsid stabilization protein
As: Gp30
At: Gp30
Au: Gp30
Av: Gp30
Aw: Gp30
Ax: Gp30
AG: HK97 gp5-like major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,87871
Polymers473,59420
Non-polymers1,28451
Water00
1
AA: HK97 gp5-like major capsid protein
AB: HK97 gp5-like major capsid protein
AC: HK97 gp5-like major capsid protein
AD: HK97 gp5-like major capsid protein
AE: HK97 gp5-like major capsid protein
AF: HK97 gp5-like major capsid protein
AI: Capsid stabilization protein
AJ: Capsid stabilization protein
AK: Capsid stabilization protein
AL: Capsid stabilization protein
AM: Capsid stabilization protein
AN: Capsid stabilization protein
AO: Capsid stabilization protein
As: Gp30
At: Gp30
Au: Gp30
Av: Gp30
Aw: Gp30
Ax: Gp30
AG: HK97 gp5-like major capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)28,492,6634260
Polymers28,415,6271200
Non-polymers77,0363060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
HK97 gp5-like major capsid protein


Mass: 43544.406 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6T9
#2: Protein
Capsid stabilization protein


Mass: 13888.911 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6Q7
#3: Protein
Gp30 / Gene product 30


Mass: 11926.760 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Haloferax tailed virus 1 / References: UniProt: A0A410N6V5
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
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-#3 / 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 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
9REFMAC5.8.0267model refinement
10UCSF ChimeraXmodel refinement
11ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2512500 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL

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