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- EMDB-9685: Cryo-EM structure of Echovirus 6 complexed with its attachment re... -

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Basic information

Entry
Database: EMDB / ID: EMD-9685
TitleCryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
Map dataCryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
Sample
  • Complex: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: Complement decay-accelerating factor
  • Ligand: SPHINGOSINE
KeywordsEchovirus 6 / CD55 / Cryo-EM / virus-receptor complex / 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 / COPI-mediated anterograde transport ...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 / COPI-mediated anterograde transport / complement activation, classical pathway / 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 speciesEchovirus E6 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGao GF / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Cell / Year: 2019
Title: Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B.
Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / ...Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / Yan Li / Meifan Zhang / Jianxun Qi / Han Wang / Ning Du / Yan Wu / Yuhai Bi / Shan Gao / Yi Shi / Jinghua Yan / Yong Zhang / Zhengde Xie / Wensheng Wei / George F Gao /
Abstract: Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for ...Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for coxsackievirus B in EV-B have been identified, receptors mediating virus entry, especially the uncoating process of echovirus and other EV-B remain obscure. Here, we found that human neonatal Fc receptor (FcRn) is the uncoating receptor for major EV-B. FcRn binds to the virus particles in the "canyon" through its FCGRT subunit. By obtaining multiple cryo-electron microscopy structures at different stages of virus entry at atomic or near-atomic resolution, we deciphered the underlying mechanisms of enterovirus attachment and uncoating. These structures revealed that different from the attachment receptor CD55, binding of FcRn to the virions induces efficient release of "pocket factor" under acidic conditions and initiates the conformational changes in viral particle, providing a structural basis for understanding the mechanisms of enterovirus entry.
History
DepositionOct 18, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.074
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.074
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ilk
  • Surface level: 0.074
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ilk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9685.png

Downloads & links

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Map

FileDownload / File: emd_9685.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.074 / Movie #1: 0.074
Minimum - Maximum-0.30402854 - 0.50333226
Average (Standard dev.)0.0014042926 (±0.023407359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3040.5030.001

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of Echovirus 6 complexed with its attachment re...

EntireName: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
Components
  • Complex: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
    • Protein or peptide: Complement decay-accelerating factor
  • Ligand: SPHINGOSINE

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Supramolecule #1: Cryo-EM structure of Echovirus 6 complexed with its attachment re...

SupramoleculeName: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Echovirus E6

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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: Echovirus E6
Molecular weightTheoretical: 31.707332 KDa
SequenceString: VVRVADTMPS GPSNSESIPA LTAAETGHTS QVVPSDTIQT RHVRNFHVRS ESSVENFLSR SACVYIVEYK TRDDTPDKMY DSWVINTRQ VAQLRRKLEF FTYVRFDVEV TFVITSVQDD STRQNTDTPA LTHQIMYVPP GGPIPQAVDD YNWQTSTNPS V FWTEGNAP ...String:
VVRVADTMPS GPSNSESIPA LTAAETGHTS QVVPSDTIQT RHVRNFHVRS ESSVENFLSR SACVYIVEYK TRDDTPDKMY DSWVINTRQ VAQLRRKLEF FTYVRFDVEV TFVITSVQDD STRQNTDTPA LTHQIMYVPP GGPIPQAVDD YNWQTSTNPS V FWTEGNAP PRMSIPFMSV GNAYSNFYDG WSHFSQTGVY GFNTLNNMGK LYFRHVNDKT ISPITSKVRI YFKPKHVKAW VP RPPRLCE YTHKDNVDFE PKGVTTSRTQ LTISNSTHVE N

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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: Echovirus E6
Molecular weightTheoretical: 28.06452 KDa
SequenceString: SDRVRSITLG NSTITTQESA NVVVGYGVWP DYLSDEEATA EDQPTQPDVA TCRFYTLDSV SWMKESQGWW WKFPDALRDM GLFGQNMQY HYLGRSGYTI HVQCNASKFH QGCLLVVCVP EAEMGAANIN EKINREHLSN GEVANTFSGT KSSNTNDVQQ A VFNAGMGV ...String:
SDRVRSITLG NSTITTQESA NVVVGYGVWP DYLSDEEATA EDQPTQPDVA TCRFYTLDSV SWMKESQGWW WKFPDALRDM GLFGQNMQY HYLGRSGYTI HVQCNASKFH QGCLLVVCVP EAEMGAANIN EKINREHLSN GEVANTFSGT KSSNTNDVQQ A VFNAGMGV AVGNLTIFPH QWINLRTNNC ATIVMPYINS VPMDNMFRHY NFTLMIIPFA KLDYAAGSST YIPITVTVAP MC AEYNGLR LAGHQ

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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: Echovirus E6
Molecular weightTheoretical: 26.378936 KDa
SequenceString: GLPVMNTPGS NQFLTSDDYQ SPTAMPQFDV TPEMNIPGEV KNLMEIAEVD SVVPVNNVNE NVNSLEAYRI PVHSVTETGA QVFGFTLQP GADTVMERTL LGEILNYYAN WSGSIKLTFM YCGSAMATGK FLLAYSPPGA GVPKNRREAM LGTHIIWDIG L QSSCVLCV ...String:
GLPVMNTPGS NQFLTSDDYQ SPTAMPQFDV TPEMNIPGEV KNLMEIAEVD SVVPVNNVNE NVNSLEAYRI PVHSVTETGA QVFGFTLQP GADTVMERTL LGEILNYYAN WSGSIKLTFM YCGSAMATGK FLLAYSPPGA GVPKNRREAM LGTHIIWDIG L QSSCVLCV PWISQTHYRF VSKDIYTDAG FITCWYQTSI VVPAEVQNQS VILCFVSACN DFSVRLLRDS PFVRQTAFYQ

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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: Echovirus E6
Molecular weightTheoretical: 7.338014 KDa
SequenceString:
GAQVSTQKTG AHETSLSASG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM VKSLPALN

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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: 21.307959 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CNRSCEVPTR LNSASLKQPY ITQNYFPVGT VVEYECRPGY RREPSLSPKL TCLQNLKWST AVEFCKKKSC PNPGEIRNGQ IDVPGGILF GATISFSCNT GYKLFGSTSS FCLISGSSVQ WSDPLPECRE IYCPAPPQID NGIIQGERDH YGYRQSVTYA C NKGFTMIG ...String:
CNRSCEVPTR LNSASLKQPY ITQNYFPVGT VVEYECRPGY RREPSLSPKL TCLQNLKWST AVEFCKKKSC PNPGEIRNGQ IDVPGGILF GATISFSCNT GYKLFGSTSS FCLISGSSVQ WSDPLPECRE IYCPAPPQID NGIIQGERDH YGYRQSVTYA C NKGFTMIG EHSIYCTVNN DEGEWSGPPP ECRG

UniProtKB: Complement decay-accelerating factor

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Macromolecule #6: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28528
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6ilk:
Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4

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