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- EMDB-47497: Asymmetric unit of yPOWV -

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Basic information

Entry
Database: EMDB / ID: EMD-47497
TitleAsymmetric unit of yPOWV
Map dataVolume map for sub-particle reconstruction of yPOWV
Sample
  • Virus: Powassan virus
    • Protein or peptide: E glycoprotein
    • Protein or peptide: Membrane Protei
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. ...Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDeer tick virus / Powassan virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsDas S / Hafenstein S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: Atomic-resolution structure of a chimeric Powassan tick-borne flavivirus
Authors: Das S / Narayanan A / Wang A / Moustafa IM / Cho SH / Mitzel D / Jose J / Hafenstein SL
History
DepositionOct 24, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47497.png

Downloads & links

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Map

FileDownload / File: emd_47497.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume map for sub-particle reconstruction of yPOWV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 350 pix.
= 427. Å		1.22 Å/pix.
x 350 pix.
= 427. Å		1.22 Å/pix.
x 350 pix.
= 427. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.335
Minimum - Maximum-2.322122 - 3.4939992
Average (Standard dev.)0.012670486 (±0.09347948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 427.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map for sub-particle reconstruction of yPOWV

Fileemd_47497_additional_1.map
AnnotationSharpened map for sub-particle reconstruction of yPOWV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A for sub-particle reconstruction of yPOWV

Fileemd_47497_half_map_1.map
AnnotationHalf-map A for sub-particle reconstruction of yPOWV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B for sub-particle reconstruction of yPOWV

Fileemd_47497_half_map_2.map
AnnotationHalf-map B for sub-particle reconstruction of yPOWV
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Powassan virus

EntireName: Powassan virus
Components
  • Virus: Powassan virus
    • Protein or peptide: E glycoprotein
    • Protein or peptide: Membrane Protei
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Powassan virus

SupramoleculeName: Powassan virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11083 / Sci species name: Powassan virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: E glycoprotein

MacromoleculeName: E glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Deer tick virus
Molecular weightTheoretical: 53.913516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TRCTHLENRD FVTGVQGTTR VSLVLELGGC VTITAEGKPS IDVWLEDIFQ ESPAETREYC LHAKLSNTKV EARCPTTGPA TLPEEHQAN MVCKRDQSDR GWGNHCGFFG KGSIVACAKF ECEEAKKAVG HVYDSTKITY VVKVEPHTGD YQAANETNEN R KTAQFTVA ...String:
TRCTHLENRD FVTGVQGTTR VSLVLELGGC VTITAEGKPS IDVWLEDIFQ ESPAETREYC LHAKLSNTKV EARCPTTGPA TLPEEHQAN MVCKRDQSDR GWGNHCGFFG KGSIVACAKF ECEEAKKAVG HVYDSTKITY VVKVEPHTGD YQAANETNEN R KTAQFTVA SEKVILDLGD YGDVSLTCKV ASGIDVAQTV VMSLGSSKDH LPSAWQLHRD WFEDLALPWK HKDNQDWNSV EK LVEFGPP HAVKMDIFNL GDQTAVLLKS LAGVPLASVD NQKYHLKSGH VTCDVGLEKL KLKGTTYSMC DKTKFKWKRV PVD SGHDTV VMEVSYTGSD KPCRIPVRAV AHGVPTINVA MLITPNPTIE TSGGGFIEMQ LPPGDNIIYV GDLSQQWFQK GSTI GRMFE KTRKGLERLS VVGEHAWDFG SVGGILSSVG KAIHTVLGGA FNTLFGGVGF IPKMLLGVAL VWLGLNARNP TMSMT FLAV GALTLMMTMG

UniProtKB: Genome polyprotein

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Macromolecule #2: Membrane Protei

MacromoleculeName: Membrane Protei / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Deer tick virus
Molecular weightTheoretical: 8.418004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SVVIPTHAQK DMVGRGHAWL KGDNIRDHVT RVEGWMWKNK LLTVAVVALA WLMLDSWMAR VTVILLALSL GPVYA

UniProtKB: Genome polyprotein

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Macromolecule #5: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 6 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5o6a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2177061
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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