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- EMDB-32195: Coxsackievirus B3(VP3-234N) incubate with CD55 at pH7.4 -

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Basic information

Entry
Database: EMDB / ID: EMD-32195
TitleCoxsackievirus B3(VP3-234N) incubate with CD55 at pH7.4
Map data
Sample
  • Complex: Coxsackievirus B3
    • Complex: Complement decay-accelerating factor
      • Protein or peptide: Complement decay-accelerating factor
    • 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
  • Ligand: PALMITIC ACID
KeywordsCVB3 / VIRUS
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
Similarity search - Domain/homology
Complement decay-accelerating factor
Similarity search - Component
Biological speciesCoxsackievirus B3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 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 13, 2021-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7vy6
  • Surface level: 0.02
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7vy6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32195.png

Downloads & links

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Map

FileDownload / File: emd_32195.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.)
1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å		1.08 Å/pix.
x 432 pix.
= 466.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.06966249 - 0.13128151
Average (Standard dev.)0.0012083689 (±0.008613462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-216-216
Dimensions432432432
Spacing432432432
CellA=B=C: 466.56003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z466.560466.560466.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-216-216-216
NC/NR/NS432432432
D min/max/mean-0.0700.1310.001

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Supplemental data

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Mask #1

Fileemd_32195_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: Complement decay-accelerating factor
      • Protein or peptide: Complement decay-accelerating factor
    • 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
  • Ligand: PALMITIC ACID

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Supramolecule #1: Coxsackievirus B3

SupramoleculeName: Coxsackievirus B3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Coxsackievirus B3

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Supramolecule #3: Complement decay-accelerating factor

SupramoleculeName: Complement decay-accelerating factor / 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: 31.703477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVEDVITAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTVENFLCR SACVYFTEYK NSGSKRYAE WVVTTRQAAQ LRRKLEFFTY IRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF ...String:
GPVEDVITAA IGRVADTVGT GPTNSEAIPA LTAAETGHTS QVVPGDTMQT RHVKNYHSRS ESTVENFLCR SACVYFTEYK NSGSKRYAE WVVTTRQAAQ LRRKLEFFTY IRFDLELTFV ITSTQQPSTT QNQDAQILTH QIMYVPPGGP VPDKVDSYVW Q TSTNPSVF WTEGNAPPRM SIPFLSIGNA YSNFYDGWSE FSRNGVYGIN TLNNMGTLYA RHVNTGSTGP IKSTIRIYFK PK HVKAWIP RPPRLCQYEK AKNVNFQPSG VTTTRQSITT 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: 28.862561 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPD YLKDSEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DAAKEFAGEP I ASGSNKLV ...String:
SPTVEECGYS DRVRSITLGN STITTQECAN VVVGYGVWPD YLKDSEATAE DQPTQPDVAT CRFYTLDSVQ WQKTSPGWWW KLPDALSNL GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCATLDN TPSSAELLGG DAAKEFAGEP I ASGSNKLV QRVVYNAGMG IGVGNLTIFP HQWINLRTNN SATIVMPYTN SVPMDNMFRH NNITLMVIPF VPLDYCPGST TY VPITVTI APMCAEYNGL RLASHQ

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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: 26.128633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMKIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI ...String:
GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMKIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVVWDVG L QSSCVLCI PWISQTHYRY VASDEYTAGG FITCWYQTNI VVPADAQSSC YIMCFVSACN DFSVRLLKDT PFISQNSFFQ

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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: 7.437209 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ATRQDFAQDP GKFTEPVKDI MIKSLPALN

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Macromolecule #5: Complement decay-accelerating factor

MacromoleculeName: Complement decay-accelerating factor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.641074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DCGLPPDVPN AQPALEGRTS FPEDTVITYK CEESFVKIPG EKDSVICLKG SQWSDIEEFC NRSCEVPTRL NSASLKQPYI TQNYFPVGT VVEYECRPGY RREPSLSPKL TCLQNLKWST AVEFCKKKSC PNPGEIRNGQ IDVPGGILFG ATISFSCNTG Y KLFGSTSS ...String:
DCGLPPDVPN AQPALEGRTS FPEDTVITYK CEESFVKIPG EKDSVICLKG SQWSDIEEFC NRSCEVPTRL NSASLKQPYI TQNYFPVGT VVEYECRPGY RREPSLSPKL TCLQNLKWST AVEFCKKKSC PNPGEIRNGQ IDVPGGILFG ATISFSCNTG Y KLFGSTSS FCLISGSSVQ WSDPLPECRE IYCPAPPQID NGIIQGERDH YGYRQSVTYA CNKGFTMIGE HSIYCTVNND EG EWSGPPP ECRGHHHHHH

UniProtKB: Complement decay-accelerating factor

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 34135
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-7vy6:
Coxsackievirus B3(VP3-234N) incubate with CD55 at pH7.4

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