+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31045 | |||||||||
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Title | Echovirus3 empty expanded particle in complex with 5G3 fab | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Echovirus E3 / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Feng R | |||||||||
Citation | Journal: Cell Discov / Year: 2021 Title: Structural basis for neutralization of an anicteric hepatitis associated echovirus by a potent neutralizing antibody. Authors: Rui Feng / Lei Wang / Dawei Shi / Binyang Zheng / Li Zhang / Hai Hou / Deju Xia / Lunbiao Cui / Xiangxi Wang / Sihong Xu / Kang Wang / Ling Zhu / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31045.map.gz | 304 MB | EMDB map data format | |
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Header (meta data) | emd-31045-v30.xml emd-31045.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_31045.png | 100 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31045 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31045 | HTTPS FTP |
-Related structure data
Related structure data | 7eajMC 7eahC 7eaiC 7eakC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31045.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.312 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Echovirus E3 in complex with 5G3 fab
Entire | Name: Echovirus E3 in complex with 5G3 fab |
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Components |
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-Supramolecule #1: Echovirus E3 in complex with 5G3 fab
Supramolecule | Name: Echovirus E3 in complex with 5G3 fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Echovirus E3
Supramolecule | Name: Echovirus E3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Echovirus E3 |
-Supramolecule #3: FAB
Supramolecule | Name: FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 32.801801 KDa |
Sequence | String: GDVEEAIDRA VARVADTMPT GPRNTESVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRT ESSIENFLCR AACVYIATYK SAGGTPTER YASWRINTRQ MVQLRRKFEL FTYLRFDMEI TFVITSTQDP GTQLAQDMPV LTHQIMYIPP GGPVPNSATD F AWQSSTNP ...String: GDVEEAIDRA VARVADTMPT GPRNTESVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRT ESSIENFLCR AACVYIATYK SAGGTPTER YASWRINTRQ MVQLRRKFEL FTYLRFDMEI TFVITSTQDP GTQLAQDMPV LTHQIMYIPP GGPVPNSATD F AWQSSTNP SIFWTEGCAP ARMSVPFISI GNAYSNFYDG WSHFTQEGVY GFNSLNNMGH IYVRHVNEQS LGVSTSTLRV YF KPKHVRA WVPRPPRLSP YVKSSNVNFK PTAVTTERKD INDVGTLRPV GYTNH |
-Macromolecule #2: VP0
Macromolecule | Name: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 36.605734 KDa |
Sequence | String: GAQVSTQKTG AHETSLTASG NSTIHYTNIN YYKDAASNSA NRQDFTQDPS KFTEPMKDVM IKSLPALNSP TVEECGFSDR VRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL F GQNMEYHY ...String: GAQVSTQKTG AHETSLTASG NSTIHYTNIN YYKDAASNSA NRQDFTQDPS KFTEPMKDVM IKSLPALNSP TVEECGFSDR VRSITLGNS TITTQECANV VVGYGVWPSY LQDNEATAED QPTQPDVATC RFYTLDSIQW QKESDGWWWK FPEALKNMGL F GQNMEYHY LGRSGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSDVERE VVAASLSSED TAKSFSRTES NGQHTVQTVV YN AGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHYNF TLMIIPFAKL EYTEQASNYV PITVTVAPMC AEY NGLRLA SHQ |
-Macromolecule #3: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E3 |
Molecular weight | Theoretical: 26.264879 KDa |
Sequence | String: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMKIPGEV HNLMEIAEVD SVVPVNNTKE NINSMEAYRI PVTGGDQLHT QVFGFQMQP GLNSVFKRTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA SPPQNRKQAM LGTHVIWDVG L QSSCVLCI ...String: GLPTMLTPGS NQFLTSDDFQ SPSAMPQFDV TPEMKIPGEV HNLMEIAEVD SVVPVNNTKE NINSMEAYRI PVTGGDQLHT QVFGFQMQP GLNSVFKRTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA SPPQNRKQAM LGTHVIWDVG L QSSCVLCI PWISQTHYRL VQQDEYTSAG YVTCWYQTGL IVPPGAPPSC TILCFASACN DFSVRNLRDT PFIEQTQLLQ |
-Macromolecule #4: heavy chain of 5G3 fab
Macromolecule | Name: heavy chain of 5G3 fab / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.298743 KDa |
Sequence | String: LQQSGAELAR PWASVKISCQ AFYTFNSYGM QWVKQRPGQG LEWIGTIYPG NGQTSYNQRF KGKATLTADK SPSTAYMQLI SLTSEDSAG CFCAVVPTVD FDYWGQGTLV TVS |
-Macromolecule #5: light chain of 5G3 fab
Macromolecule | Name: light chain of 5G3 fab / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.828412 KDa |
Sequence | String: DIVMSQSPSS LAVSVWEKVT MSCKSSQSLL YSNTQKNYLA WYQQKPGQSP KLLIYWASTR ESGVPDRFTG SGSGTDFTLT ISSVKAEDL AVYYCQQYYS YPLTFGAGTK LELKRA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41237 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |