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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3631 | ||||||||||||
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Title | CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa | ||||||||||||
![]() | CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa | ||||||||||||
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Function / homology | ![]() icosahedral viral capsid / modulation by virus of host chromatin organization / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Kotecha A / Stuart D | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14 KB | Display | ![]() |
Images | ![]() | 295.3 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nejMC ![]() 3630C ![]() 3632C ![]() 3633C ![]() 3634C ![]() 3635C ![]() 5ne4C ![]() 5nedC ![]() 5nemC ![]() 5nerC ![]() 5netC ![]() 5neuC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoEM Structure of Foot and Mouth Disease Virus O1 Manisa | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Foot-and-mouth disease virus
Entire | Name: ![]() ![]() ![]() |
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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 / Sci species strain: O1 Manisa / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() ![]() |
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: O1 Manisa VP1
Macromolecule | Name: O1 Manisa VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 23.222348 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPEAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGESKYGDG TVANVRGDLQ VLAQKAARAL P TSFNYGAI ...String: TTSAGESADP VTATVENYGG ETQVQRRQHT DVSFILDRFV KVTPKDQINV LDLMQTPAHT LVGALLRTAT YYFADLEVAV KHEGNLTWV PNGAPEAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGESKYGDG TVANVRGDLQ VLAQKAARAL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAIHPDQ ARHKQKIVAP VKQ UniProtKB: Genome polyprotein |
-Macromolecule #2: O1 Manisa VP2
Macromolecule | Name: O1 Manisa VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 24.41751 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVAQAER FFKTHLFDWV TSDPFGRCHL LELPTDHKG VYGYLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIQKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY ...String: DKKTEETTLL EDRILTTRNG HTTSTTQSSV GVTYGYATAE DFVSGPNTSG LETRVAQAER FFKTHLFDWV TSDPFGRCHL LELPTDHKG VYGYLTDSYA YMRNGWDVEV TAVGNQFNGG CLLVAMVPEL CSIQKRELYQ LTLFPHQFIN PRTNMTAHIT V PFVGVNRY DQYKVHKPWT LVVMVVAPLT VNSEGAPQIK VYANIAPTNV HVAGEFPSKE UniProtKB: Genome polyprotein |
-Macromolecule #3: O1 Manisa VP3
Macromolecule | Name: O1 Manisa VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 23.933879 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYT ...String: GIFPVACSDG YGGLVTTDPK TADPAYGKVF NPPRNMLPGR FTNFLDVAEA CPTFLHFEGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYT YTASDVAETT NVQGWVCLFQ ITHGKADGDA LVVLASAGKD FELRLPVDAR TQ UniProtKB: Genome polyprotein |
-Macromolecule #4: O1 Manisa VP1
Macromolecule | Name: O1 Manisa VP1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 8.766075 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NATSGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Sample stage | Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
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 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |