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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3862 | |||||||||
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Title | FMDV A10 dissociated pentamer | |||||||||
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![]() | FMDV A10 dissociated pentamer != Foot-and-mouth disease virus (strain A10-61) FMDV A10 dissociated pentamer
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![]() | A10 / FMDV / Pentamer / CryoEM / virus / VIRAL PROTEIN | |||||||||
Function / homology | ![]() L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / 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 / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
![]() | Kotecha A / Malik N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of foot and mouth disease virus pentamers: Insight into capsid dissociation and unexpected pentamer reassociation. Authors: Nayab Malik / Abhay Kotecha / Sarah Gold / Amin Asfor / Jingshan Ren / Juha T Huiskonen / Tobias J Tuthill / Elizabeth E Fry / David I Stuart / ![]() ![]() Abstract: Foot-and-mouth disease virus (FMDV) belongs to the Aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious ...Foot-and-mouth disease virus (FMDV) belongs to the Aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products. FMDV capsids (which are unstable below pH6.5) release their genome into the host cell from an acidic compartment, such as that of an endosome, and in the process dissociate into pentamers. Whilst other members of the family (enteroviruses) have been visualized to form an expanded intermediate capsid with holes from which inner capsid proteins (VP4), N-termini (VP1) and RNA can be released, there has been no visualization of any such state for an aphthovirus, instead the capsid appears to simply dissociate into pentamers. Here we present the 8-Å resolution structure of isolated dissociated pentamers of FMDV, lacking VP4. We also found these pentamers to re-associate into a rigid, icosahedrally symmetric assembly, which enabled their structure to be solved at higher resolution (5.2 Å). In this assembly, the pentamers unexpectedly associate 'inside out', but still with their exposed hydrophobic edges buried. Stabilizing interactions occur between the HI loop of VP2 and its symmetry related partners at the icosahedral 3-fold axes, and between the BC and EF loops of VP3 with the VP2 βB-strand and the CD loop at the 2-fold axes. A relatively extensive but subtle structural rearrangement towards the periphery of the dissociated pentamer compared to that in the mature virus provides insight into the mechanism of dissociation of FMDV and the marked difference in antigenicity. | |||||||||
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 | ![]() | 28.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.2 KB 17.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7 KB | Display | ![]() |
Images | ![]() | 160.3 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oyiMC ![]() 3856C ![]() 5owxC 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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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 : FMDV A10 dissociated pentamer
Entire | Name: FMDV A10 dissociated pentamer |
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Components |
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-Supramolecule #1: Foot-and-mouth disease virus (strain A10-61)
Supramolecule | Name: Foot-and-mouth disease virus (strain A10-61) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12112 Sci species name: Foot-and-mouth disease virus (strain A10-61) Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 455 kDa/nm |
Virus shell | Shell ID: 1 / Name: Foot and Disease Virus A1061 / Diameter: 30.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: L-peptidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.09798 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: RHHTDVGFIM DRFVKINSLS PTHVIDLMQT HKHGIVGALL RAATYYFSDL EIVVRHDGNL TWVPNGAPEA ALSNTSNPTA YNKAPFTRL ALPYTAPHRV LATVYDGTNK YSASDSRSGD LGSIAARVAT QLPASFNYGA IQAQAIHELL VRMKRAELYC P RPLLAIKV TSQDRYKQKI IAPA UniProtKB: Genome polyprotein |
-Macromolecule #2: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO / EC number: L-peptidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.701512 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SVGVTYGYST EEDHVAGPNT SGLETRVVQA ERFFKKFLFD WTTDKPFGYL TKLELPTDHH GVFGHLVDSY AYMRNGWDVE VSAVGNQFN GGCLLVAMVP EWKAFDTREK YQLTLFPHQF ISPRTNMTAH ITVPYLGVNR YDQYKKHKPW TLVVMVLSPL T VSNTAAPQ IKVYANIAPT YVHV UniProtKB: Genome polyprotein |
-Macromolecule #3: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO / EC number: L-peptidase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.233992 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: GIFPVACADG YGGLVTTDPK TADPVYGKVY NPPKTNYPGR FTNLLDVAEA CPTFLRFDDG KPYVVTRADD TRLLAKFDVS LAAKHMSNT YLSGIAQYYT QYSGTINLHF MFTGSTDSKA RYMVAYIPPG VETPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String: GIFPVACADG YGGLVTTDPK TADPVYGKVY NPPKTNYPGR FTNLLDVAEA CPTFLRFDDG KPYVVTRADD TRLLAKFDVS LAAKHMSNT YLSGIAQYYT QYSGTINLHF MFTGSTDSKA RYMVAYIPPG VETPPDTPEE AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDTAET TNVQGWVCVY QITHGKAEND TLLVSASAGK DFELRLPIDP RTQ UniProtKB: Genome polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 8 / Details: 50mM Hepes, 200mM NaCl |
Grid | Model: C-Flats R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 6 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 18 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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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: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 1570 / Average exposure time: 5.0 sec. / Average electron dose: 20.0 e/Å2 |
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 / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 200 / Target criteria: Cross-correlation coefficient |
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Output model | ![]() PDB-5oyi: |