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- EMDB-0856: Cryo-EM structure of echovirus 11 complexed with its attaching re... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0856 | |||||||||
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Title | Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 | |||||||||
![]() | Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 | |||||||||
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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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule 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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / transport vesicle / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / positive regulation of T cell cytokine production / symbiont-mediated suppression of host gene expression / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / positive regulation of cytosolic calcium ion concentration / DNA replication / host cell cytoplasm / RNA helicase activity / symbiont entry into host cell / induction by virus of host autophagy / membrane raft / RNA-directed RNA polymerase / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / Neutrophil degranulation / virion attachment to host cell / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
![]() | Liu S / Gao FG | |||||||||
![]() | ![]() Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn. Authors: Niu S / Liu C / Liu C / Liu S / Song Y / Zhang Y / Tian W / Zhao X / Wang P / Gao FG | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 202.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.8 KB 12.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 22.5 KB | Display | ![]() |
Images | ![]() | 263.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6la5MC ![]() 0854C ![]() 0855C ![]() 0857C ![]() 0858C ![]() 0859C ![]() 0860C ![]() 0867C ![]() 0870C ![]() 0871C ![]() 6la3C ![]() 6la4C ![]() 6la6C ![]() 6la7C ![]() 6laoC ![]() 6lapC ![]() 6lb1C ![]() 6lboC ![]() 6lbqC 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 11 complexed with its attaching receptor CD55 at pH 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 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 : Echovirus E11
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Echovirus E11
Supramolecule | Name: Echovirus E11 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#5 / NCBI-ID: 12078 / Sci species name: Echovirus E11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-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: 32.277359 KDa |
Sequence | String: VVEAVENAVA RVADTISSGP SNSQAVPALT AVETGHTSQV TPSDTIQTRH VRNYHSRSES SIENFLCRSA CVYMGEYHTT NTDTSKLFA SWTINARRMV QMRRKLELFT YVRFDMEVTF VITSKQDQGT QLGQDMPPLT HQIMYIPPGG PIPKSVTDYT W QTSTNPSI ...String: VVEAVENAVA RVADTISSGP SNSQAVPALT AVETGHTSQV TPSDTIQTRH VRNYHSRSES SIENFLCRSA CVYMGEYHTT NTDTSKLFA SWTINARRMV QMRRKLELFT YVRFDMEVTF VITSKQDQGT QLGQDMPPLT HQIMYIPPGG PIPKSVTDYT W QTSTNPSI FWTEGNAPPR MSIPFISIGN AYSNFYDGWS HFSQNGVYGY NTLNHMGQIY VRHVNGSSPL PMTSTVRMYF KP KHVKVWV PRPPRLCQYK NASTVNFTPT NITEKRQSIN YIPETVKP |
-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: 27.968449 KDa |
Sequence | String: DRVRSITLGN STITTQESAN VVVAYGRWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVT WERDSPGWWW KFPDALKDMG LFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLMVVCVPE AEMGCSQVDG TVNEHSLSEG ETAKKFASTS TNGTNTVQSI V TNAGMGVG ...String: DRVRSITLGN STITTQESAN VVVAYGRWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVT WERDSPGWWW KFPDALKDMG LFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLMVVCVPE AEMGCSQVDG TVNEHSLSEG ETAKKFASTS TNGTNTVQSI V TNAGMGVG VGNLTIFPHQ WINLRTNNCA TIVMPYINNV PMDNMFRHHN FTLMIIPFVP LDYSSDSSTY VPITVTVAPM CA EYNGLRL ATSL |
-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: 26.062578 KDa |
Sequence | String: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI ...String: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELNIPGEV QNLMEIAEVD SVVPVNNVEG KLDTMEIYRI PVQSGNHQSS QVFGFQVQP GLDNVFKHTL LGEILNYYAH WSGSIKLTFV FCGSAMATGK FLLAYAPPGA NAPKSRKDAM LGTHIIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG NVTCWYQTGI VVPAGTPTSC SIMCFVSACN DFSVRLLKDT PFIEQSALLQ |
-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: 7.495273 KDa |
Sequence | String: MGAQVSTQKT GAHETGLNAS GRSIIHYTNI NYYKDAASNS ANRQDFSQDP GKFTEPVKDI MVKSLPALN |
-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: 13.586049 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: KSCPNPGEIR NGQIDVPGGI LFGATISFSC NTGYKLFGST SSFCLISGSS VQWSDPLPEC REIYCPAPPQ IDNGIIQGER DHYGYRQSV TYACNKGFTM IGEHSIYCTV NNDEGEWSGP PPECRG |
-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: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 1.025 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 |