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- PDB-7vy6: Coxsackievirus B3(VP3-234N) incubate with CD55 at pH7.4 -

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Basic information

Entry
Database: PDB / ID: 7vy6
TitleCoxsackievirus B3(VP3-234N) incubate with CD55 at pH7.4
Components
  • (Capsid protein ...) x 4
  • Complement decay-accelerating factor
KeywordsVIRUS / CVB3
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / ficolin-1-rich granule membrane / complement activation, classical pathway / COPI-mediated anterograde transport / side of membrane / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Complement decay-accelerating factor
Similarity search - Component
Biological speciesCoxsackievirus B3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 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 13, 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.title / _citation.year / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Aug 10, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 16, 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 / _pdbx_entry_details.has_protein_modification

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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
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-32195
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-32195
  • 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: Complement decay-accelerating factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0296
Polymers122,7735
Non-polymers2561
Water00
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: Complement decay-accelerating factor
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,381,763360
Polymers7,366,377300
Non-polymers15,38560
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: Complement decay-accelerating factor
hetero molecules
x 5


  • icosahedral pentamer
  • 615 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)615,14730
Polymers613,86525
Non-polymers1,2825
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: Complement decay-accelerating factor
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 738 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)738,17636
Polymers736,63830
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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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein Capsid protein VP1


Mass: 31703.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein Capsid protein VP2


Mass: 28862.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Capsid protein VP3


Mass: 26128.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Protein Capsid protein VP4


Mass: 7437.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 2 molecules E

#5: Protein Complement decay-accelerating factor


Mass: 28641.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD55, CR, DAF / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P08174
#6: 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 B3COMPLEX#1-#50RECOMBINANT
2Capsid protein VP1, VP2, VP3, VP4VIRUS#1-#41RECOMBINANT
3Complement decay-accelerating factorCOMPLEX#51RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Coxsackievirus B312072
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293
32Homo sapiens (human)9606HEK293
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

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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34135 / 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

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