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- EMDB-18599: Portal protein of full Haloferax tailed virus 1. -

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Basic information

Entry
Database: EMDB / ID: EMD-18599
TitlePortal protein of full Haloferax tailed virus 1.
Map data
Sample
  • Virus: Haloferax tailed virus 1
    • Protein or peptide: HK97 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: Portal protein
  • Ligand: MAGNESIUM ION
KeywordsArchaeal virus / portal / portal capsid interface / Mg ions / VIRUS
Function / homologyPortal protein / HK97 gp6-like/SPP1 gp15-like head-tail connector
Function and homology information
Biological speciesHaloferax tailed virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.342 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 5, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18599.png

Downloads & links

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Map

FileDownload / File: emd_18599.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: 0.011
Minimum - Maximum-0.023245769 - 0.053695537
Average (Standard dev.)0.0004133576 (±0.003551805)
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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Additional map: EMReady map

Fileemd_18599_additional_1.map
AnnotationEMReady map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18599_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18599_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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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 gp6-like/SPP1 gp15-like head-tail connector
    • Protein or peptide: Portal protein
  • 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-#2 / 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 gp6-like/SPP1 gp15-like head-tail connector

MacromoleculeName: HK97 gp6-like/SPP1 gp15-like head-tail connector / type: protein_or_peptide / ID: 1 / 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 #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / 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 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: 2.342 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165198
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-8qqn:
Portal protein of full Haloferax tailed virus 1.

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