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- EMDB-32209: Coxsackievirus B3 at pH7.4 (VP3-234E) incubation with coxsackievi... -

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Basic information

Entry
Database: EMDB / ID: EMD-32209
TitleCoxsackievirus B3 at pH7.4 (VP3-234E) incubation with coxsackievirus and adenovirus receptor for 10min
Map data
Sample
  • Complex: Coxsackievirus B3
    • Complex: Coxsackievirus and adenovirus receptor
      • Protein or peptide: Coxsackievirus and adenovirus receptor
    • Virus: Homo sapiens (human)
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4
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 / 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 / germ cell migration / apicolateral plasma membrane / 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 / germ cell migration / apicolateral plasma membrane / 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 / mitochondrion organization / Cell surface interactions at the vascular wall / PDZ domain binding / adherens junction / neuromuscular junction / beta-catenin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / integrin binding / cell junction / virus receptor activity / heart development / 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
: / 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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor
Similarity search - Component
Biological speciesCoxsackievirus B3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7vym
  • Surface level: 0.01
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vym
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Structure viewerEM map:
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Supplemental images

emd_32209.png

Downloads & links

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Map

FileDownload / File: emd_32209.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.)
1.1 Å/pix.
x 432 pix.
= 475.2 Å		1.1 Å/pix.
x 432 pix.
= 475.2 Å		1.1 Å/pix.
x 432 pix.
= 475.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.01
Minimum - Maximum-0.0517521 - 0.091939606
Average (Standard dev.)0.00093260355 (±0.0060379184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-216-216
Dimensions432432432
Spacing432432432
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z475.200475.200475.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-216-216-216
NC/NR/NS432432432
D min/max/mean-0.0520.0920.001

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Supplemental data

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Mask #1

Fileemd_32209_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: Coxsackievirus and adenovirus receptor
      • Protein or peptide: Coxsackievirus and adenovirus receptor
    • Virus: Homo sapiens (human)
      • Protein or peptide: Capsid protein VP1
      • Protein or peptide: Capsid protein VP2
      • Protein or peptide: Capsid protein VP3
      • Protein or peptide: Capsid protein VP4

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Supramolecule #1: Coxsackievirus B3

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

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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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Supramolecule #2: Homo sapiens

SupramoleculeName: Homo sapiens / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / NCBI-ID: 9606 / Sci species name: Homo sapiens / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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: 31.561285 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVEDAVTAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTVENFLCR SACVYFTEYK NSGSKRYAE WVVTTRQAAQ LRRKLEFFTY IRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF ...String:
GPVEDAVTAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTVENFLCR SACVYFTEYK NSGSKRYAE WVVTTRQAAQ LRRKLEFFTY IRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF WTEGNAPPRM SIPFLSIGNA YSNFYDGWSD FSRDGVYGIN TLNSMGTLYA RHVNTGGTGP IKSTIRIYFK PK HVKAWIP RPPRLCQYEK AKNVNFQPSG VTTTRQSITA MTNTGAF

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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: 28.85649 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPD YLKDNEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DAAKEFAGEP I ASGSNKLV ...String:
SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPD YLKDNEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DAAKEFAGEP I ASGSNKLV QRVVYNAGMG IGVGNLTIFP HQWINLRTNN SATIVMPYTN SVPMDNMFRH NNVTLMVIPF VPLDYCPGST TY VPITVTI APMNAEYNGL RLAGHQ

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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: 26.154695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPLGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI ...String:
GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPLGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI PWISQTHYRY VASDECTAGG FITCWYQTNI VVPADAQSSC YIMCFVSACN DFSVRLLKDT PFISQENFFQ

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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: 7.306014 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GAQVSTQKTG AHETGLNASG NSIIHYTNIN YYKDAASNSA TRQDFAQDPG KFTEPVKDIM IKSLPALN

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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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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: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 54522
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-7vym:
Coxsackievirus B3 at pH7.4 (VP3-234E) incubation with coxsackievirus and adenovirus receptor for 10min

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