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- PDB-7dq7: Cryo-EM structure of Coxsackievirus B1 mature virion in complex w... -

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Basic information

Entry
Database: PDB / ID: 7dq7
TitleCryo-EM structure of Coxsackievirus B1 mature virion in complex with nAb 5F5
Components
  • 5F5 VH
  • 5F5 VL
  • Capsid protein VP4
  • VP2
  • VP3
  • Virion protein 1
KeywordsVIRUS/IMMUNE SYSTEM / Coxsackievirus B1 / CAR / Cryo-EM / neutralizing antibody / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / 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 / Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B1
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
Revision 1.0May 5, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0May 5, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 5, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
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Revision 2.0Jun 18, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
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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
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Virion protein 1
B: VP2
C: VP3
D: Capsid protein VP4
L: 5F5 VL
H: 5F5 VH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1257
Polymers118,8686
Non-polymers2561
Water00
1
A: Virion protein 1
B: VP2
C: VP3
D: Capsid protein VP4
L: 5F5 VL
H: 5F5 VH
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,147,477420
Polymers7,132,092360
Non-polymers15,38560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area24340 Å2
ΔGint-126 kcal/mol
Surface area43570 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Virion protein 1
B: VP2
C: VP3
D: Capsid protein VP4
L: 5F5 VL
H: 5F5 VH
hetero molecules
x 5


  • icosahedral pentamer
  • 596 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)595,62335
Polymers594,34130
Non-polymers1,2825
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Virion protein 1
B: VP2
C: VP3
D: Capsid protein VP4
L: 5F5 VL
H: 5F5 VH
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 715 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)714,74842
Polymers713,20936
Non-polymers1,5396
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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

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Protein , 4 types, 4 molecules ABCD

#1: Protein Virion protein 1 / 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 / VP4


Mass: 7484.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B1 / References: UniProt: A0A2S1FMR1

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Antibody , 2 types, 2 molecules LH

#5: Antibody 5F5 VL


Mass: 11218.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Antibody 5F5 VH


Mass: 13506.880 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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Details

Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Coxsackievirus B1 complex with nAb 5F5COMPLEX#1-#60MULTIPLE SOURCES
2Coxsackievirus B1COMPLEX#1-#41NATURAL
3nAb 5F5COMPLEX#5-#61NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Coxsackievirus B112071
33Mus musculus (house mouse)10090
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 FIELD
Image recordingElectron dose: 25 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3259: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2814 / Symmetry type: POINT

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