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Yorodumi- EMDB-15920: Complex of Echovirus 11 with its attaching receptor decay-acceler... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15920 | |||||||||
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Title | Complex of Echovirus 11 with its attaching receptor decay-accelerating factor (CD55) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Echovirus E11 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Stuart DI / Ren J / Zhou D / Qin L | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Viruses / Year: 2022 Title: Switching of Receptor Binding Poses between Closely Related Enteroviruses. Authors: Daming Zhou / Ling Qin / Helen M E Duyvesteyn / Yuguang Zhao / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Kuan-Ying A Huang / David I Stuart / Abstract: Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity ...Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity and mortality. Decay-accelerating factor (DAF, also known as CD55) is an attachment receptor for E11. Here, we report the structure of the complex of E11 and the full-length ectodomain of DAF (short consensus repeats, SCRs, 1-4) at 3.1 Å determined by cryo-electron microscopy (cryo-EM). SCRs 3 and 4 of DAF interact with E11 at the southern rim of the canyon via the VP2 EF and VP3 BC loops. We also observe an unexpected interaction between the N-linked glycan (residue 95 of DAF) and the VP2 BC loop of E11. DAF is a receptor for at least 20 enteroviruses and we classify its binding patterns from reported DAF/virus complexes into two distinct positions and orientations, named as E6 and E11 poses. Whilst 60 DAF molecules can attach to the virion in the E6 pose, no more than 30 can attach to E11 due to steric restrictions. Analysis of the distinct modes of interaction and structure and sequence-based phylogenies suggests that the two modes evolved independently, with the E6 mode likely found earlier. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15920.map.gz | 226.8 MB | EMDB map data format | |
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Header (meta data) | emd-15920-v30.xml emd-15920.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_15920.png | 67.7 KB | ||
Others | emd_15920_half_map_1.map.gz emd_15920_half_map_2.map.gz | 159.1 MB 159 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15920 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15920 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15920.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_15920_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15920_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Echovirus 11 with its attaching receptor DECAY ACCELER...
Entire | Name: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55) |
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Components |
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-Supramolecule #1: Complex of Echovirus 11 with its attaching receptor DECAY ACCELER...
Supramolecule | Name: Complex of Echovirus 11 with its attaching receptor DECAY ACCELERATING FACTOR (CD55) type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Echovirus E11 |
-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 E11 |
Molecular weight | Theoretical: 32.838828 KDa |
Sequence | String: GDVVEAIEGA VARVADTISS GPTNSQAVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLSR SACVYMGEYY TTNTDETKR FASWTINARR MVQMRRKLEM FTYVRFDVEV TFVITSKQDQ GTQLGQDMPP LTHQIMYIPP GGPIPKSTTD Y AWQTSTNP ...String: GDVVEAIEGA VARVADTISS GPTNSQAVPA LTAVETGHTS QVVPGDTMQT RHVKNYHSRS ESTIENFLSR SACVYMGEYY TTNTDETKR FASWTINARR MVQMRRKLEM FTYVRFDVEV TFVITSKQDQ GTQLGQDMPP LTHQIMYIPP GGPIPKSTTD Y AWQTSTNP SIFWTEGNAP PRMSIPFVSI GNAYSNFYDG WSHFSQNGVY GYNTLNNMGQ LYMRHVNGPS PLPMTSIVRV YF KPKHVKA WVPRPPRLCQ YKNASTVNFS STNITDKRDS ITHVPDTVKP DVTTH |
-Macromolecule #2: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E11 |
Molecular weight | Theoretical: 28.886428 KDa |
Sequence | String: SPSAEECGYS DRVRSITLGN STITTQECAN VVVAYGRWPE YLSDKEATAE DQPTQPDVAT CRFYTLESVT WEKDSPGWWW KFPDALKDM GLFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSDVGG TVNEHAISEG EIAKKFSATA T NGAHTVQS ...String: SPSAEECGYS DRVRSITLGN STITTQECAN VVVAYGRWPE YLSDKEATAE DQPTQPDVAT CRFYTLESVT WEKDSPGWWW KFPDALKDM GLFGQNMYYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSDVGG TVNEHAISEG EIAKKFSATA T NGAHTVQS IVTNAGMGVG VGNLTIYPHQ WVNLRTNNSA TIVMPYINSV PMDNMFRHHN FTLMIIPFVS LDYSSDASTY VP ITVTVAP MCAEYNGLRL ATSLQ |
-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 E11 |
Molecular weight | Theoretical: 26.029674 KDa |
Sequence | String: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELDIPGEV KNLMEIAEVD SVVPVNNVVG KLDTMDIFRI PVQSGNHQST QVFGFQVQP GLDSVFKHTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA NAPKTRKDAM LGTHVIWDVG L QSSCVLCI ...String: GLPVMNTPGS NQFLTSDDFQ SPSAMPQFDV TPELDIPGEV KNLMEIAEVD SVVPVNNVVG KLDTMDIFRI PVQSGNHQST QVFGFQVQP GLDSVFKHTL LGEILNYYAH WSGSVKLTFV FCGSAMATGK FLLAYSPPGA NAPKTRKDAM LGTHVIWDVG L QSSCVLCI PWISQTHYRL VHQDEYTSAG NVTCWYQTGI VVPAGTPTLC SIMCFVSACN DFSVRLLKDT PFIEQSALLQ |
-Macromolecule #4: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Echovirus E11 |
Molecular weight | Theoretical: 7.498273 KDa |
Sequence | String: MGAQVSTQKT GAHETGLNAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP GKFTEPVKDI MIKSMPALN |
-Macromolecule #5: DECAY ACCELERATING FACTOR (CD55)
Macromolecule | Name: DECAY ACCELERATING FACTOR (CD55) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.771059 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: (MSE)GCVAETGDC GLPPDVPNAQ PALEGRTSFP EDTVITYKCE ESFVKIPGEK DSVICLKGSQ WSDIEEFCNR SCEVPT RLN SASLKQPYIT QNYFPVGTVV EYECRPGYRR EPSLSPKLTC LQNLKWSTAV EFCKKKSCPN PGEIRNGQID VPGGILF GA TISFSCNTGY ...String: (MSE)GCVAETGDC GLPPDVPNAQ PALEGRTSFP EDTVITYKCE ESFVKIPGEK DSVICLKGSQ WSDIEEFCNR SCEVPT RLN SASLKQPYIT QNYFPVGTVV EYECRPGYRR EPSLSPKLTC LQNLKWSTAV EFCKKKSCPN PGEIRNGQID VPGGILF GA TISFSCNTGY KLFGSTSSFC LISGSSVQWS DPLPECREIY CPAPPQIDNG IIQGERDHYG YRQSVTYACN KGFT (MSE)IGEH SIYCTVNNDE GEWSGPPPEC RGGTKHHHHH H |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 3.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6394 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |