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- EMDB-32207: Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievi... -

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Basic information

Entry
Database: EMDB / ID: EMD-32207
TitleCoxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min
Map data
Sample
  • Complex: Coxsackievirus B3
    • Complex: Capsid protein VP1, VP2, VP3, VP4
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4
    • Complex: coxsackievirus and adenovirus receptor
      • Protein or peptide: Coxsackievirus and adenovirus receptor
  • Ligand: PALMITIC ACID
KeywordsCVB3 / VIRUS
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / symbiont-mediated perturbation of host transcription / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / symbiont-mediated perturbation of host transcription / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport / cell-cell junction organization / connexin binding / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / intercalated disc / bicellular tight junction / cell adhesion molecule binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / neutrophil chemotaxis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / acrosomal vesicle / PDZ domain binding / Cell surface interactions at the vascular wall / filopodium / adherens junction / mitochondrion organization / 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 / neuromuscular junction / beta-catenin binding / host cell cytoplasmic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / cell junction / cell-cell junction / nucleoside-triphosphate phosphatase / heart development / virus receptor activity / cell body / actin cytoskeleton organization / channel activity / growth cone / monoatomic ion transmembrane transport / basolateral plasma membrane / symbiont-mediated suppression of host NF-kappaB cascade / defense response to virus / DNA replication / RNA helicase activity / neuron projection / membrane raft / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / signaling receptor binding / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / protein-containing complex / ATP hydrolysis activity / proteolysis / extracellular space / RNA binding / extracellular region / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Picornavirus coat protein VP4 superfamily / Immunoglobulin domain / Picornavirus coat protein / 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 coat protein VP4 superfamily / Immunoglobulin domain / Picornavirus coat protein / 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) / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Immunoglobulin V-set domain / 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 / Immunoglobulin V-set domain / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin subtype / Immunoglobulin / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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 / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesCoxsackievirus B3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsWang QL / Liu CC
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)82072289 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Molecular basis of differential receptor usage for naturally occurring CD55-binding and -nonbinding coxsackievirus B3 strains.
Authors: Qingling Wang / Qian Yang / Congcong Liu / Guoqing Wang / Hao Song / Guijun Shang / Ruchao Peng / Xiao Qu / Sheng Liu / Yingzi Cui / Peiyi Wang / Wenbo Xu / Xin Zhao / Jianxun Qi / Mengsu Yang / George F Gao /
Abstract: Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay- ...Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay-accelerating factor (DAF; CD55) to infect cells. However, the differential receptor usage mechanism for CVB remains elusive. This study identified VP3-234 residues (234Q/N/V/D/E) as critical population selection determinants during CVB3 virus evolution, contributing to diverse binding affinities to CD55. Cryoelectron microscopy (cryo-EM) structures of CD55-binding/nonbinding isolates and their complexes with CD55 or CAR were obtained under both neutral and acidic conditions, and the molecular mechanism of VP3-234 residues determining CD55 affinity/specificity for naturally occurring CVB3 strains was elucidated. Structural and biochemical studies in vitro revealed the dynamic entry process of CVB3 and the function of the uncoating receptor CAR with different pH preferences. This work provides detailed insight into the molecular mechanism of CVB infection and contributes to an in-depth understanding of enterovirus attachment receptor usage.
History
DepositionNov 14, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7vyk
  • Surface level: 0.015
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vyk
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32207.png

Downloads & links

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Map

FileDownload / File: emd_32207.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.10906482 - 0.17054984
Average (Standard dev.)0.0009751111 (±0.010378027)
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 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z466.560466.560466.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-216-216-216
NC/NR/NS432432432
D min/max/mean-0.1090.1710.001

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Supplemental data

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Mask #1

Fileemd_32207_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
  • Complex: Coxsackievirus B3
    • Complex: Capsid protein VP1, VP2, VP3, VP4
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4
    • Complex: coxsackievirus and adenovirus receptor
      • Protein or peptide: Coxsackievirus and adenovirus receptor
  • Ligand: PALMITIC ACID

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Supramolecule #1: Coxsackievirus B3

SupramoleculeName: Coxsackievirus B3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Coxsackievirus B3

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Supramolecule #2: Capsid protein VP1, VP2, VP3, VP4

SupramoleculeName: Capsid protein VP1, VP2, VP3, VP4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: coxsackievirus and adenovirus receptor

SupramoleculeName: coxsackievirus and adenovirus receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5

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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: 30.05366 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYENS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI ...String:
RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYENS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI PFLSIGNAYS NFYDGWSEFS RNGVYGINTL NNMGTLYARH VNAGSTGPIK STIRIYFKPK HVKAWIPRPP RL CQYEKAK NVNFQPSGVT TTRQSITTMT

UniProtKB: Genome polyprotein

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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

UniProtKB: Genome polyprotein

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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

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B3
Molecular weightTheoretical: 7.480235 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MIKSLPALN

UniProtKB: Genome polyprotein

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Macromolecule #5: Coxsackievirus and adenovirus receptor

MacromoleculeName: Coxsackievirus and adenovirus receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.106408 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSITTPEEMI EKAKGETAYL PCKFTLSPED QGPLDIEWLI SPADNQKVDQ VIILYSGDKI YDDYYPDLKG RVHFTSNDLK SGDASINVT NLQLSDIGTY QCKVKKAPGV ANKKIHLVVL VKPSGARCYV DGSEEIGSDF KIKCEPKEGS LPLQYEWQKL S DSQKMPTS ...String:
MSITTPEEMI EKAKGETAYL PCKFTLSPED QGPLDIEWLI SPADNQKVDQ VIILYSGDKI YDDYYPDLKG RVHFTSNDLK SGDASINVT NLQLSDIGTY QCKVKKAPGV ANKKIHLVVL VKPSGARCYV DGSEEIGSDF KIKCEPKEGS LPLQYEWQKL S DSQKMPTS WLAEMTSSVI SVKNASSEYS GTYSCTVRNR VGSDQCLLRL NVVPPSNKAL EHHHHHH

UniProtKB: Coxsackievirus and adenovirus receptor

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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
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
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 FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 158446
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1cov

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 35532
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 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 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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1cov

chain_id: A, source_name: PDB, initial_model_type: experimental model

1cov

chain_id: B, source_name: PDB, initial_model_type: experimental model

1cov

chain_id: C, source_name: PDB, initial_model_type: experimental model

1cov

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7vyk:
Coxsackievirus B3 at pH7.4 (VP3-234Q) incubation with coxsackievirus and adenovirus receptor for 10min

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