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- EMDB-39895: Yeast-expressed polio type 2 stabilized virus-like particles -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39895
TitleYeast-expressed polio type 2 stabilized virus-like particles
Map data
Sample
  • Complex: Poliovirus 2
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
  • Ligand: SPHINGOSINE
KeywordsPoliovirus type 2 / virus-like particles / compact state / VIRAL PROTEIN
Function / homology
Function and homology information


picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression ...picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / channel activity / viral capsid / monoatomic ion transmembrane transport / RNA helicase activity / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHong Q / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: High-yield production, immunogenicity and structure of yeast-expressed polio type 2 stabilized virus-like particles
Authors: Hong Q / Wang SX / Wang XL / Han WY / Chen T / Liu Y / Cheng F / Qin S / Zhao ST / Liu QW / Cong Y / Huang Z
History
DepositionApr 26, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39895.png

Downloads & links

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Map

FileDownload / File: emd_39895.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 488 pix.
= 533.384 Å		1.09 Å/pix.
x 488 pix.
= 533.384 Å		1.09 Å/pix.
x 488 pix.
= 533.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.047589343 - 0.048275437
Average (Standard dev.)0.000009425523 (±0.0024927824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions488488488
Spacing488488488
CellA=B=C: 533.38403 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39895_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39895_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39895_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Poliovirus 2

EntireName: Poliovirus 2
Components
  • Complex: Poliovirus 2
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
  • Ligand: SPHINGOSINE

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Supramolecule #1: Poliovirus 2

SupramoleculeName: Poliovirus 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Yeast-expressed polio type 2 stablized virus-like particles
Source (natural)Organism: Poliovirus 2

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Poliovirus 2
Molecular weightTheoretical: 33.073246 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLGDLIEGVV EGVTRNALTP LTPANNLPDT QSSGPAHSKE IPALTAVETG ATNPLVPSDT VQTRHVIQKR TRSESTVESF FARGACVAI IEVDNDAPTK RASKLFSVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT SNYTDANNGH ALNQVYQIMF I PPGAPIPG ...String:
GLGDLIEGVV EGVTRNALTP LTPANNLPDT QSSGPAHSKE IPALTAVETG ATNPLVPSDT VQTRHVIQKR TRSESTVESF FARGACVAI IEVDNDAPTK RASKLFSVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT SNYTDANNGH ALNQVYQIMF I PPGAPIPG KWNDYTWQTS SNPSVFYTYG APPARISVPY VGIANAYSHF YDGFAKVPLA GQASTEGDSL YGAASLNDFG SL AVRVVND HNPTKLTSKI RVYMKPKHVR VWCPRPPRAV PYYGPGVDYK DGLAPLPEKG LTTY

UniProtKB: Genome polyprotein

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Macromolecule #2: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 2
Molecular weightTheoretical: 26.49134 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVLNTPGS NQYLTADNYQ SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT PILCFSLSP ASDPRLAHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA EAPKSRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVLNTPGS NQYLTADNYQ SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT PILCFSLSP ASDPRLAHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA EAPKSRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRL TINDSFTEGG YISMFYQTRV VVPLSTPRKM DILGFVSACN DFSVRLLRDT THISQEAMPQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Poliovirus 2
Molecular weightTheoretical: 29.996779 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: SPNIEACGYS DRVMQLTLGN STITTQEAAN SVVAYGRWPE YIKDSEANPV DQPTEPDVAA CRFYTLDTVT WRKESRGWWW KLPDALKDM GLFGQNMFYH YLGRAGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSTTH MFTKYENANP GEKGGEFKGS F TLDTNATN ...String:
SPNIEACGYS DRVMQLTLGN STITTQEAAN SVVAYGRWPE YIKDSEANPV DQPTEPDVAA CRFYTLDTVT WRKESRGWWW KLPDALKDM GLFGQNMFYH YLGRAGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSTTH MFTKYENANP GEKGGEFKGS F TLDTNATN PARNFCPVDY LFGSGVLAGN AFVYPHQIIN LRTNNCATLV LPYVNSLSID SMTKHNNWGI AILPLAPLDF AT ESSTEIP ITLTIAPMCC EFNGLRNITV PRTQ

UniProtKB: Genome polyprotein

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Macromolecule #4: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Startup model#0 - Type of model: EMDB MAP
#0 - EMDB ID:

3747


#1 - Type of model: EMDB MAP
#1 - EMDB ID:

3747

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
Startup model#0 - Type of model: EMDB MAP
#0 - EMDB ID:

3747


#1 - Type of model: EMDB MAP
#1 - EMDB ID:

3747

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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