+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30845 | |||||||||
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Title | FMDV capsid in complex with M170 Nab | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Foot-and-mouth disease virus / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Dong H / Liu P | |||||||||
Funding support | China, 1 items
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Citation | Journal: Protein Cell / Year: 2022 Title: Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies. Authors: Hu Dong / Pan Liu / Manyuan Bai / Kang Wang / Rui Feng / Dandan Zhu / Yao Sun / Suyu Mu / Haozhou Li / Michiel Harmsen / Shiqi Sun / Xiangxi Wang / Huichen Guo / | |||||||||
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_30845.map.gz | 166.7 MB | EMDB map data format | |
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Header (meta data) | emd-30845-v30.xml emd-30845.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_30845.png | 68.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30845 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30845 | HTTPS FTP |
-Validation report
Summary document | emd_30845_validation.pdf.gz | 634.2 KB | Display | EMDB validaton report |
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Full document | emd_30845_full_validation.pdf.gz | 633.8 KB | Display | |
Data in XML | emd_30845_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_30845_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30845 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30845 | HTTPS FTP |
-Related structure data
Related structure data | 7dstMC 7dssC 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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-Map
File | Download / File: emd_30845.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : FMDV in complex with M170
Entire | Name: FMDV in complex with M170 |
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Components |
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-Supramolecule #1: FMDV in complex with M170
Supramolecule | Name: FMDV in complex with M170 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Foot-and-mouth disease virus |
-Supramolecule #2: FMDV
Supramolecule | Name: FMDV / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Lama glama (llama) |
-Supramolecule #3: M170
Supramolecule | Name: M170 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5 |
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-Macromolecule #1: VP1 of O type FMDV capsid
Macromolecule | Name: VP1 of O type FMDV capsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 22.849139 KDa |
Sequence | String: TTSTGESADP VTATVENYGG ETQVQRRHHT DVSFILDRFV KVTPKDSINV LDLMQTPSHT LVGALLRTAT YYFADLEVAV KHKGDLTWV PNGAPVAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGKCKYAEG SLPNVRGDLQ VLAQKAARPL P TSFNYGAI ...String: TTSTGESADP VTATVENYGG ETQVQRRHHT DVSFILDRFV KVTPKDSINV LDLMQTPSHT LVGALLRTAT YYFADLEVAV KHKGDLTWV PNGAPVAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGKCKYAEG SLPNVRGDLQ VLAQKAARPL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAVHPSA ARHKQKIVAP |
-Macromolecule #2: VP2 of O type FMDV capsid
Macromolecule | Name: VP2 of O type FMDV capsid / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 23.091078 KDa |
Sequence | String: RILTTRNGHT TSTTQSSVGI THGYATAEDF VNGPNTSGLE TRVVQAERFF KTHLFDWVTS DPFGRYYLLE LPTDHKGVYG SLTDSYAYM RNGWDVEVTA VGNQFNGGCL LVAMVPELCS IEQRELFQLT LFPHQFINPR TNMTAHIKVP FVGVNRYDQY K VHKPWTLV ...String: RILTTRNGHT TSTTQSSVGI THGYATAEDF VNGPNTSGLE TRVVQAERFF KTHLFDWVTS DPFGRYYLLE LPTDHKGVYG SLTDSYAYM RNGWDVEVTA VGNQFNGGCL LVAMVPELCS IEQRELFQLT LFPHQFINPR TNMTAHIKVP FVGVNRYDQY K VHKPWTLV VMVVAPLTVN TEGAPQIKVY ANIAPTNVHV AGEFPSKE |
-Macromolecule #3: VP3 of O type FMDV capsid
Macromolecule | Name: VP3 of O type FMDV capsid / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 23.754705 KDa |
Sequence | String: GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNMLPGR FTNLLDVAEA CPTFLHFDGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTVNLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String: GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNMLPGR FTNLLDVAEA CPTFLHFDGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTVNLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDAAETT NVQGWVCLFQ ITHGKAEGDA LVVLASAGKD FELRLPVDAR Q |
-Macromolecule #4: VP4 of O type FMDV capsid
Macromolecule | Name: VP4 of O type FMDV capsid / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Foot-and-mouth disease virus |
Molecular weight | Theoretical: 7.963328 KDa |
Sequence | String: SQNQSGNTGS IINNYYMQQY QNSMDTQLGN NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA |
-Macromolecule #5: M170 Nab
Macromolecule | Name: M170 Nab / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 12.939211 KDa |
Recombinant expression | Organism: Lama glama (llama) |
Sequence | String: GGSQVQLQES GGGLVQAGGS LRLSCAASGR TFSSYAMGWF RQAPGSEREF VARISWSGGS TYYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC TAGFALPPSD YWGQGTQVTV SS |
-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 TITAN KRIOS |
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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: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3692 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |