[English] 日本語
Yorodumi- EMDB-0856: Cryo-EM structure of echovirus 11 complexed with its attaching re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0856 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 | |||||||||
Map data | Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 | |||||||||
Sample |
| |||||||||
Keywords | Cryo-EM structure / echovirus 11 / CD55 / pH 7.4 / 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) / 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 / COPI-mediated anterograde transport / complement activation, classical pathway / side of membrane / transport vesicle / picornain 2A / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / secretory granule membrane / T=pseudo3 icosahedral viral capsid / Regulation of Complement cascade / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / positive regulation of T cell cytokine production / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / viral capsid / nucleoside-triphosphate phosphatase / channel activity / virus receptor activity / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / symbiont entry into host cell / membrane raft / RNA-directed RNA polymerase / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / innate immune response / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / Neutrophil degranulation / host cell nucleus / 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 | Echovirus E11 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Liu S / Gao FG | |||||||||
Citation | Journal: Chin.Sci.Bull. / Year: 2020 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0856.map.gz | 202.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0856-v30.xml emd-0856.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0856_fsc.xml | 22.5 KB | Display | FSC data file |
Images | emd_0856.png | 263.9 KB | ||
Filedesc metadata | emd-0856.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0856 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0856 | HTTPS FTP |
-Validation report
Summary document | emd_0856_validation.pdf.gz | 658.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0856_full_validation.pdf.gz | 658 KB | Display | |
Data in XML | emd_0856_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_0856_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0856 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0856 | 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 (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_0856.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM structure of echovirus 11 complexed with its attaching receptor CD55 at pH 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Echovirus E11
Entire | Name: Echovirus E11 |
---|---|
Components |
|
-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 |
---|
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Echovirus E11 |
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 |
---|---|
Source (natural) | Organism: Echovirus E11 |
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 |
---|---|
Source (natural) | Organism: Echovirus E11 |
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 |
---|---|
Source (natural) | Organism: Echovirus E11 |
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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.586049 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KSCPNPGEIR NGQIDVPGGI LFGATISFSC NTGYKLFGST SSFCLISGSS VQWSDPLPEC REIYCPAPPQ IDNGIIQGER DHYGYRQSV TYACNKGFTM IGEHSIYCTV NNDEGEWSGP PPECRG UniProtKB: Complement decay-accelerating factor |
-Macromolecule #6: SPHINGOSINE
Macromolecule | Name: SPHINGOSINE / type: ligand / ID: 6 / Number of copies: 1 / Formula: SPH |
---|---|
Molecular weight | Theoretical: 299.492 Da |
Chemical component information | ChemComp-SPH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |