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- EMDB-18559: C1 turret to capsid interface of full Haloferax tailed virus 1 ad... -

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Basic information

Entry
Database: EMDB / ID: EMD-18559
TitleC1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: Prokaryotic polysaccharide deacetylase
    • Protein or peptide: gp30
    • Protein or peptide: HK97 gp5-like major capsid protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsArchaeal virus / turret / turret capsid interface / Mg ions / VIRUS
Function / homologyNodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / HK97 gp5-like major capsid protein / Prokaryotic polysaccharide deacetylase
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 1
Authors: Zhang D / Daum B / Isupov MN / McLaren M / Oksanen H / Quax TEF / Schwarzer S / Gold VAM / Antson A
History
DepositionOct 2, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18559.png

Downloads & links

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Map

FileDownload / File: emd_18559.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 256 pix.
= 299.776 Å		1.17 Å/pix.
x 256 pix.
= 299.776 Å		1.17 Å/pix.
x 256 pix.
= 299.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.038767755 - 0.08683626
Average (Standard dev.)-0.00008577035 (±0.0073124543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 299.776 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18559_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18559_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18559_half_map_2.map
Projections & Slices
AxesZYX

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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: Prokaryotic polysaccharide deacetylase
    • Protein or peptide: gp30
    • Protein or peptide: HK97 gp5-like major capsid protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM 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-#3 / 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: Prokaryotic polysaccharide deacetylase

MacromoleculeName: Prokaryotic polysaccharide deacetylase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 45.242082 KDa
SequenceString: MTGLNPDGLG RTAAFSNTSA ESVSAVDATI DRLYAQDRIE IPTDSRQLFS TRGTVLRNFE DLSGWTANIG SLSAETSDVY VGSQSARLT ASSSAVDIRY SFGTAQDFTG KGFSMALKRI DVSGSSDSTP IKIRLVDGNT NYRTFSARCR PGGGDEWGRR D FGFESEDT ...String:
MTGLNPDGLG RTAAFSNTSA ESVSAVDATI DRLYAQDRIE IPTDSRQLFS TRGTVLRNFE DLSGWTANIG SLSAETSDVY VGSQSARLT ASSSAVDIRY SFGTAQDFTG KGFSMALKRI DVSGSSDSTP IKIRLVDGNT NYRTFSARCR PGGGDEWGRR D FGFESEDT GFDVTNVQTM TVTTNSRSSI DILVDDIRVV DSSGTGQVIV TIDDVHTGDK TAAEVFGRYG IPIGLAANAK FL DQSSSKL TTQEFKDLLA KPHVYAVNHG YNHYDYGSYS IDEIEDDVIR GKYELQDLGV REPNINHYVY PSGNYAQESI DML SNYHVM SWGTGAESFD ALTPNQLTSP WHNLRCSFDS GTAEAEQAVN DAATYNQTAH IYFHSDNVTQ SEMESVAQTI NSAD VTPIT LMDFYNQQ

UniProtKB: Prokaryotic polysaccharide deacetylase

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Macromolecule #2: gp30

MacromoleculeName: gp30 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 12.005731 KDa
SequenceString:
MTDTIVNVQG SFFSASASGV ADTESLLIDP QDAKFGAIEI HNIA(NEP)GGSVD VELLTSSDDT ELVEDAAVTL DSFTGE GIS QGNQIEASDN TNTYIRITNT SGGAIDIIAT GREVSQ

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Macromolecule #3: HK97 gp5-like major capsid protein

MacromoleculeName: HK97 gp5-like major capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 43.544406 KDa
SequenceString: MLMEAALPGS DVSAREVAKV WPGAKKGDYS FLQGNQSRSL EAEMTRTARA EAGTDRHRAL KDYAVDADNL PKTLSAGSKH LTEDGDVIE ARLDDAIPRM LFAASDPEYV DTLFREQLLE VVMEGRELRK VAREASNVIN ANTRVGDVPI ASDEEFARPT G QGAEIRDD ...String:
MLMEAALPGS DVSAREVAKV WPGAKKGDYS FLQGNQSRSL EAEMTRTARA EAGTDRHRAL KDYAVDADNL PKTLSAGSKH LTEDGDVIE ARLDDAIPRM LFAASDPEYV DTLFREQLLE VVMEGRELRK VAREASNVIN ANTRVGDVPI ASDEEFARPT G QGAEIRDD GETYTTVAWN ATKLTEGSRV TDEMRDQAMV DLIERNIQRV GASLENGINR VFLTELVDNA QNNHDTAGSN QG YQALNSA VGEVDKDDFR PDTYVTHPDY RTQLFNDTNL AYANRAGTNE VLRNREDAPI VGDIAGLDMH AAMSSATYDD GTD IGWSGG SETWGFSSDG DKGAVVYDRD NIHTILYAPN GQDVEIKDYE DPIRDITGVN GRLHVDCQYS QGRSSATVQY

UniProtKB: HK97 gp5-like major capsid protein

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 50 / Formula: MG
Molecular weightTheoretical: 24.305 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: 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102012
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Initial model type: in silico model
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-8qpq:
C1 turret to capsid interface of full Haloferax tailed virus 1 adjacent to the portal-capsid interface.

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