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- EMDB-9684: Cryo-EM structure of Echovirus 6 complexed with its attachment re... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9684 | |||||||||
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Title | Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 | |||||||||
![]() | Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 | |||||||||
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Function / homology | ![]() 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 / side of membrane ...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 / side of membrane / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / complement activation, classical pathway / 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Gao GF / Liu S / Zhao X / Peng R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 41.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.9 KB | Display | ![]() |
Images | ![]() | 83.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6iljMC ![]() 9685C ![]() 9686C ![]() 9687C ![]() 9688C ![]() 9689C ![]() 9690C ![]() 6ilkC ![]() 6illC ![]() 6ilmC ![]() 6ilnC ![]() 6iloC ![]() 6ilpC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Cryo-EM structure of Echovirus 6 complexed with its attachment re...
Entire | Name: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 |
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Components |
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-Supramolecule #1: Cryo-EM structure of Echovirus 6 complexed with its attachment re...
Supramolecule | Name: Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 5.5 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.707332 KDa |
Sequence | String: 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 |
-Macromolecule #2: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.06452 KDa |
Sequence | String: 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 |
-Macromolecule #3: Capsid protein VP3
Macromolecule | Name: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.378936 KDa |
Sequence | String: 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 |
-Macromolecule #4: Capsid protein VP4
Macromolecule | Name: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.338014 KDa |
Sequence | String: GAQVSTQKTG AHETSLSASG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM VKSLPALN |
-Macromolecule #5: Complement decay-accelerating factor
Macromolecule | Name: Complement decay-accelerating factor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 21.307959 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #6: SPHINGOSINE
Macromolecule | Name: SPHINGOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPH |
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Molecular weight | Theoretical: 299.492 Da |
Chemical component information | ![]() ChemComp-SPH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6ilj: |