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- EMDB-18642: Portal capsid interface of full Haloferax tailed virus 1. -

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Basic information

Entry
Database: EMDB / ID: EMD-18642
TitlePortal capsid interface of full Haloferax tailed virus 1.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp5-like major capsid protein
  • Protein or peptide: Capsid stabilization protein
  • Protein or peptide: Hypothetical protein gp21
  • Protein or peptide: Portal protein
  • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsArchaeal virus / portal / portal capsid interface / Mg ions / VIRUS
Function / homologyPortal protein / Capsid stabilization protein / HK97 gp6-like/SPP1 gp15-like head-tail connector / HK97 gp5-like major capsid protein
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 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 11, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18642.png

Downloads & links

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Map

FileDownload / File: emd_18642.map.gz / Format: CCP4 / Size: 166.4 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 352 pix.
= 412.192 Å		1.17 Å/pix.
x 352 pix.
= 412.192 Å		1.17 Å/pix.
x 352 pix.
= 412.192 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: 0.015
Minimum - Maximum-0.027541073 - 0.05749739
Average (Standard dev.)0.00058976107 (±0.004918915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 412.19202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18642_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18642_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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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: HK97 gp5-like major capsid protein
  • Protein or peptide: Capsid stabilization protein
  • Protein or peptide: Hypothetical protein gp21
  • Protein or peptide: Portal protein
  • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM 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 / 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: HK97 gp5-like major capsid protein

MacromoleculeName: HK97 gp5-like major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / 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 #2: Capsid stabilization protein

MacromoleculeName: Capsid stabilization protein / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 13.888911 KDa
SequenceString:
MATETQGEHT FPVEVLISGE ELRGYTAGEA LSAGEPVYLS GDYEVSASSA DGGEFLGVNL YDVASGEPVA LAGDDCEVRV EVSEQVTAN DEILPDGLGT FETVATSAAS AGVAIVQEGA ASGEVCEAYI FAVQGTTA

UniProtKB: Capsid stabilization protein

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Macromolecule #3: Hypothetical protein gp21

MacromoleculeName: Hypothetical protein gp21 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Haloferax tailed virus 1
Molecular weightTheoretical: 9.860767 KDa
SequenceString:
MQLRRSPGMR PMDRDW(HIP)QER ARAREQAYSS DLTSQFSESE IVKYELDTAQ IDGSDNPRTY IWNRTIDLFG MNGTDV REL RNR

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Macromolecule #4: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 4 / 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

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Macromolecule #5: HK97 gp6-like/SPP1 gp15-like head-tail connector

MacromoleculeName: HK97 gp6-like/SPP1 gp15-like head-tail connector / type: protein_or_peptide / ID: 5 / 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

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 183 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 17 / Formula: K
Molecular weightTheoretical: 39.098 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 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

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Image processing

Image recording ID2
DetailsDataset produced as a combination of both FALCON 4i and K3 collections
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157388
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-8qsy:
Portal capsid interface of full Haloferax tailed virus 1.

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