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- PDB-7w14: Coxsackievirus B3 at pH7.4 (VP3-234E) incubation with coxsackievi... -

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Basic information

Entry
Database: PDB / ID: 7w14
TitleCoxsackievirus B3 at pH7.4 (VP3-234E) incubation with coxsackievirus and adenovirus receptor for 20min
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
  • Coxsackievirus and adenovirus receptor
KeywordsVIRUS / CVB3 / VP3-234E / coxsackievirus and adenovirus receptor / 20min
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 / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / transepithelial transport ...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 / 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 / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / filopodium / adherens junction / mitochondrion organization / PDZ domain binding / Cell surface interactions at the vascular wall / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / integrin binding / cell junction / heart development / virus receptor activity / growth cone / cell body / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / neuron projection / membrane raft / signaling receptor binding / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Jelly Rolls - #20 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...: / Jelly Rolls - #20 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesCoxsackievirus B3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWang, Q.L. / Liu, C.C.
Funding support China, 1items
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 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-32250
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  • Superimposition on EM map
  • EMDB-32250
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: Coxsackievirus and adenovirus receptor


Theoretical massNumber of molelcules
Total (without water)118,1565
Polymers118,1565
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: Coxsackievirus and adenovirus receptor
x 60


Theoretical massNumber of molelcules
Total (without water)7,089,361300
Polymers7,089,361300
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: Coxsackievirus and adenovirus receptor
x 5


  • icosahedral pentamer
  • 591 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)590,78025
Polymers590,78025
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: Coxsackievirus and adenovirus receptor
x 6


  • icosahedral 23 hexamer
  • 709 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)708,93630
Polymers708,93630
Non-polymers00
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

#1: Protein Capsid protein VP1 / P1D / Virion protein 1


Mass: 31561.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Homo sapiens (human)
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 28856.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Homo sapiens (human)
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26154.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Homo sapiens (human)
#4: Protein Capsid protein VP4 / P1A / Virion protein 4


Mass: 7306.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Homo sapiens (human)
#5: Protein Coxsackievirus and adenovirus receptor / CAR / hCAR / CVB3-binding protein / Coxsackievirus B-adenovirus receptor / HCVADR


Mass: 24277.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CXADR, CAR / Production host: Homo sapiens (human) / References: UniProt: P78310
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 B3 incubation with coxsackievirus and adenovirus receptorCOMPLEXall0RECOMBINANT
2Coxsackievirus B3VIRUS#1-#41RECOMBINANT
3receptorCOMPLEX#51RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Coxsackievirus B312072
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN1particle selectionethan.py was used to automatically pick particles
2EPUimage acquisitionEPU was used to collect the raw data
4CTFFIND4CTF correctionCTFFIND4 was used to estimate the CTF values
7UCSF Chimera1.14model fitting
9PHENIX1.18model refinement
10RELION3.0.8initial Euler assignmentRELION 3.0.8 was used to determine the initial angular assignment
11RELION3.0.8final Euler assignmentRELION 3.0.8 was used to determine the final angular assignment
12RELION3.0.8classificationRELION 3.0.8 was used to do Class3D
13RELION3.0.83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 158446
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57633 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 1COV / Initial refinement model-ID: 1 / PDB-ID: 1COV

1cov

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
3C
4D
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0077534
ELECTRON MICROSCOPYf_angle_d0.92810274
ELECTRON MICROSCOPYf_dihedral_angle_d6.8054468
ELECTRON MICROSCOPYf_chiral_restr0.0611144
ELECTRON MICROSCOPYf_plane_restr0.0061334

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