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- EMDB-32183: Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-32183
TitleCoxsackievirus B3 A-particle at pH7.4 (VP3-234Q)
Map data
Sample
  • Virus: Coxsackievirus B3
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
Function / homology
Function and homology information


: / symbiont-mediated perturbation of host gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / T=pseudo3 icosahedral viral capsid ...: / symbiont-mediated perturbation of host gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
Biological speciesCoxsackievirus B3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang QL / Liu CC
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82072289 China
CitationJournal: To Be Published
Title: Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q)
Authors: Wang QL / Liu CC
History
DepositionNov 12, 2021-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32183.png

Downloads & links

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Map

FileDownload / File: emd_32183.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.034
Minimum - Maximum-0.10506019 - 0.18807544
Average (Standard dev.)0.0013812126 (±0.010117523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-216-216
Dimensions432432432
Spacing432432432
CellA=B=C: 466.56003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32183_msk_1.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 : Coxsackievirus B3

EntireName: Coxsackievirus B3
Components
  • Virus: Coxsackievirus B3
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Coxsackievirus B3

SupramoleculeName: Coxsackievirus B3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12072 / Sci species name: Coxsackievirus B3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Homo sapiens (human)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B3
Molecular weightTheoretical: 31.639371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVEDAITAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLCR SACVYFTEYE NSGAKRYAE WVLTPRQAAQ LRRKLEFFTY VRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF ...String:
GPVEDAITAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLCR SACVYFTEYE NSGAKRYAE WVLTPRQAAQ LRRKLEFFTY VRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF WTEGNAPPRM SIPFLSIGNA YSNFYDGWSE FSRNGVYGIN TLNNMGTLYA RHVNAGSTGP IKSTIRIYFK PK HVKAWIP RPPRLCQYEK AKNVNFQPSG VTTTRQSITT MTNTGAF

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B3
Molecular weightTheoretical: 28.822475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPTVEECGYS DRARSITLGN STITTQECAN VVVGYGVWPD YLKDSEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DSAKEFADKP V ASGSNKLV ...String:
SPTVEECGYS DRARSITLGN STITTQECAN VVVGYGVWPD YLKDSEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTVH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DSAKEFADKP V ASGSNKLV QRVVYNAGMG VGVGNLTIFP HQWINLRTNN SATIVMPYTN SVPMDNMFRH NNVTLMVIPF VPLDYCPGST TY VPITVTI APMCAEYNGL RLAGHQ

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B3
Molecular weightTheoretical: 26.227725 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI ...String:
GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI PWISQTHYRY VTSDEYTAGG FITCWYQTNI VVPADAQSSC YIMCFVSACN DFSVRLLKDT PFISQQNFFQ

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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: 7.4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 158446
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Software - details: CTFFIND4 was used to estimate the CTF values
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1cov

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Software - details: RELION 3.0.8 was used to determine the initial angular assignment
Final 3D classificationNumber classes: 5 / Avg.num./class: 27834 / Software - Name: RELION (ver. 3.0.8) / Software - details: RELION 3.0.8 was used to do Class3D
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Software - details: RELION 3.0.8 was used to determine the final angular assignment
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 31260
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1cov

chain_id: A

1cov

chain_id: B

1cov

chain_id: C

1cov

chain_id: D
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7vxl:
Coxsackievirus B3 A-particle at pH7.4 (VP3-234Q)

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