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- PDB-7dpz: Cryo-EM structure of Coxsackievirus B1 virion in complex with CAR -

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Basic information

Entry
Database: PDB / ID: 7dpz
TitleCryo-EM structure of Coxsackievirus B1 virion in complex with CAR
Components
  • Capsid protein VP4
  • Coxsackievirus and adenovirus receptor
  • VP2
  • VP3
  • Virion protein 1Virus
KeywordsVIRUS / Coxsackievirus B1 / CAR / Cryo-EM
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 / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization ...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 / homotypic cell-cell adhesion / AV node cell to bundle of His cell communication / epithelial structure maintenance / gamma-delta T cell activation / regulation of AV node cell action potential / germ cell migration / apicolateral plasma membrane / cell-cell junction organization / transepithelial transport / 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 / bicellular tight junction / intercalated disc / picornain 2A / cell adhesion molecule binding / symbiont-mediated suppression of host mRNA export from nucleus / mitochondrion organization / symbiont genome entry into host cell via pore formation in plasma membrane / neutrophil chemotaxis / picornain 3C / acrosomal vesicle / filopodium / T=pseudo3 icosahedral viral capsid / PDZ domain binding / host cell cytoplasmic vesicle membrane / Cell surface interactions at the vascular wall / adherens junction / neuromuscular junction / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / beta-catenin binding / viral capsid / : / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / nucleoside-triphosphate phosphatase / integrin binding / virus receptor activity / protein complex oligomerization / cell junction / cell body / monoatomic ion channel activity / heart development / growth cone / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / RNA helicase activity / DNA replication / neuron projection / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / membrane raft / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / signaling receptor binding / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / protein-containing complex / proteolysis / extracellular space / RNA binding / extracellular region / nucleoplasm / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Immunoglobulin domain / 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 superfamily / Immunoglobulin domain / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Picornavirus/Calicivirus coat protein / Immunoglobulin V-set domain / Viral coat protein subunit / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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 / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Coxsackievirus and adenovirus receptor / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi, S. / Zhu, R. / Xu, L. / Cheng, T. / Zheng, Q.
CitationJournal: Cell Host Microbe / Year: 2021
Title: Cryo-EM structures reveal the molecular basis of receptor-initiated coxsackievirus uncoating.
Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing ...Authors: Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Hai Yu / Yu Lin / Yuanyuan Wu / Maozhou He / Yang Huang / Yichao Jiang / Hui Sun / Zhenghui Zha / Hongwei Yang / Qiongzi Huang / Dongqing Zhang / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Lisheng Yang / Che Liu / Yuqiong Que / Mujin Fang / Ying Gu / Jun Zhang / Wenxin Luo / Z Hong Zhou / Shaowei Li / Tong Cheng / Ningshao Xia /
Abstract: Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a ...Enterovirus uncoating receptors bind at the surface depression ("canyon") that encircles each capsid vertex causing the release of a host-derived lipid called "pocket factor" that is buried in a hydrophobic pocket formed by the major viral capsid protein, VP1. Coxsackievirus and adenovirus receptor (CAR) is a universal uncoating receptor of group B coxsackieviruses (CVB). Here, we present five high-resolution cryoEM structures of CVB representing different stages of virus infection. Structural comparisons show that the CAR penetrates deeper into the canyon than other uncoating receptors, leading to a cascade of events: collapse of the VP1 hydrophobic pocket, high-efficiency release of the pocket factor and viral uncoating and genome release under neutral pH, as compared with low pH. Furthermore, we identified a potent therapeutic antibody that can neutralize viral infection by interfering with virion-CAR interactions, destabilizing the capsid and inducing virion disruption. Together, these results define the structural basis of CVB cell entry and antibody neutralization.
History
DepositionDec 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-30812
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Virion protein 1
2: VP2
3: VP3
4: Capsid protein VP4
K: Coxsackievirus and adenovirus receptor


Theoretical massNumber of molelcules
Total (without water)107,6145
Polymers107,6145
Non-polymers00
Water0
1
1: Virion protein 1
2: VP2
3: VP3
4: Capsid protein VP4
K: Coxsackievirus and adenovirus receptor
x 60


Theoretical massNumber of molelcules
Total (without water)6,456,854300
Polymers6,456,854300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area20910 Å2
ΔGint-108 kcal/mol
Surface area39050 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: Virion protein 1
2: VP2
3: VP3
4: Capsid protein VP4
K: Coxsackievirus and adenovirus receptor
x 5


  • icosahedral pentamer
  • 538 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)538,07125
Polymers538,07125
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: Virion protein 1
2: VP2
3: VP3
4: Capsid protein VP4
K: Coxsackievirus and adenovirus receptor
x 6


  • icosahedral 23 hexamer
  • 646 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)645,68530
Polymers645,68530
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Virion protein 1 / Virus / VP1 / P1C / P1D


Mass: 31207.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: W8GTF7
#2: Protein VP2


Mass: 29122.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: A0A2S0RQC2
#3: Protein VP3


Mass: 26328.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: L7UV52
#4: Protein Capsid protein VP4 /


Mass: 7484.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: A0A2S1FMR1
#5: Protein Coxsackievirus and adenovirus receptor / hCAR / CVB3-binding protein / Coxsackievirus B-adenovirus receptor / HCVADR


Mass: 13471.361 Da / Num. of mol.: 1 / Fragment: D1 domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P78310

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Coxsackievirus B1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Coxsackievirus B1
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6538 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0067359
ELECTRON MICROSCOPYf_angle_d0.57110032
ELECTRON MICROSCOPYf_dihedral_angle_d6.6484389
ELECTRON MICROSCOPYf_chiral_restr0.0451122
ELECTRON MICROSCOPYf_plane_restr0.0041295

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