+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3630 | ||||||||||||
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Title | CryoEM Structure of Foot and Mouth Disease Virus O PanAsia | ||||||||||||
Map data | CryoEM Map of FMDV O PanAsia | ||||||||||||
Sample | Foot and Mouth Disease Virus O PanAsia != Foot-and-mouth disease virus Foot and Mouth Disease Virus O PanAsia
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Keywords | Foot and Mouth Disease Virus / FMDV / virus / OpanAsia | ||||||||||||
Function / homology | Function and homology information icosahedral viral capsid / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid ...icosahedral viral capsid / modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / viral capsid / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont entry into host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Foot-and-mouth disease virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Kotecha A / Stuart D | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2017 Title: Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus. Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T ...Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T Huiskonen / David I Stuart / Abstract: Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, ...Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role. | ||||||||||||
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_3630.map.gz | 228.7 MB | EMDB map data format | |
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Header (meta data) | emd-3630-v30.xml emd-3630.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3630_fsc.xml | 14 KB | Display | FSC data file |
Images | emd_3630.png | 286.9 KB | ||
Filedesc metadata | emd-3630.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3630 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3630 | HTTPS FTP |
-Validation report
Summary document | emd_3630_validation.pdf.gz | 317.5 KB | Display | EMDB validaton report |
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Full document | emd_3630_full_validation.pdf.gz | 316.6 KB | Display | |
Data in XML | emd_3630_validation.xml.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3630 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3630 | HTTPS FTP |
-Related structure data
Related structure data | 5nedMC 3631C 3632C 3633C 3634C 3635C 5ne4C 5nejC 5nemC 5nerC 5netC 5neuC 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_3630.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM Map of FMDV O PanAsia | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Foot and Mouth Disease Virus O PanAsia
Entire | Name: Foot and Mouth Disease Virus O PanAsia |
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Components |
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-Supramolecule #1: Foot-and-mouth disease virus
Supramolecule | Name: Foot-and-mouth disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12110 / Sci species name: Foot-and-mouth disease virus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 9 MDa |
Virus shell | Shell ID: 1 / Name: Foot and Mouth Disease virus / Diameter: 300.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: O PanAsia VP1
Macromolecule | Name: O PanAsia VP1 / 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: 23.341467 KDa |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
Sequence | String: TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATA YNGNCKYGES HTTNVRGDLQ VLAQKAARTL P TSFNYGAI ...String: TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPETALD NTTNPTAYHK APLTRLALPY TAPHRVLATA YNGNCKYGES HTTNVRGDLQ VLAQKAARTL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIHPSE ARHKQKIVAP VKQ UniProtKB: Genome polyprotein |
-Macromolecule #2: O PanAsia VP2
Macromolecule | Name: O PanAsia VP2 / 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: 24.389453 KDa |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
Sequence | String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATTE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDSFGRCHL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSINKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY ...String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATTE DFVSGPNTSG LETRVVQAER FFKTHLFDWV TSDSFGRCHL LELPTDHKG VYGSLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSINKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNTEGAPQIK VYANIAPTNV HVAGEFPSKE UniProtKB: Genome polyprotein |
-Macromolecule #3: O PanAsia VP3
Macromolecule | Name: O PanAsia VP3 / 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: 23.938898 KDa |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
Sequence | String: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLRFEGD VPYVTTKTDS DRILAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLRFEGD VPYVTTKTDS DRILAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDTAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ UniProtKB: Genome polyprotein |
-Macromolecule #4: O PanAsia VP4
Macromolecule | Name: O PanAsia VP4 / 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: 8.791128 KDa |
Recombinant expression | Organism: Cricetinae gen. sp. (mammal) |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSNHTT NTQNNDWFSK LASSAFSGLF GALLA UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 50.0 mM / Component - Name: HEPES |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Energy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 360 / Average exposure time: 5.0 sec. / Average electron dose: 18.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000 |
Sample stage | Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 120 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-5ned: |