+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14519 | ||||||||||||
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Title | VP2-only capsid of wt MVM prototype strain p | ||||||||||||
Map data | VP2-only capsid of wt MVM prototype strain p sharpened map | ||||||||||||
Sample |
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Function / homology | Function and homology information permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Minute virus of mice | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||||||||
Authors | Luque D / Ortega-Esteban A / Valbuena A / Vilas JL / Rodriguez-Huete A / Mateu MG / Caston JR | ||||||||||||
Funding support | Spain, 3 items
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Citation | Journal: J Mol Biol / Year: 2023 Title: Equilibrium Dynamics of a Biomolecular Complex Analyzed at Single-amino Acid Resolution by Cryo-electron Microscopy. Authors: Daniel Luque / Alvaro Ortega-Esteban / Alejandro Valbuena / Jose Luis Vilas / Alicia Rodríguez-Huete / Mauricio G Mateu / José R Castón / Abstract: The biological function of macromolecular complexes depends not only on large-scale transitions between conformations, but also on small-scale conformational fluctuations at equilibrium. Information ...The biological function of macromolecular complexes depends not only on large-scale transitions between conformations, but also on small-scale conformational fluctuations at equilibrium. Information on the equilibrium dynamics of biomolecular complexes could, in principle, be obtained from local resolution (LR) data in cryo-electron microscopy (cryo-EM) maps. However, this possibility had not been validated by comparing, for a same biomolecular complex, LR data with quantitative information on equilibrium dynamics obtained by an established solution technique. In this study we determined the cryo-EM structure of the minute virus of mice (MVM) capsid as a model biomolecular complex. The LR values obtained correlated with crystallographic B factors and with hydrogen/deuterium exchange (HDX) rates obtained by mass spectrometry (HDX-MS), a gold standard for determining equilibrium dynamics in solution. This result validated a LR-based cryo-EM approach to investigate, with high spatial resolution, the equilibrium dynamics of biomolecular complexes. As an application of this approach, we determined the cryo-EM structure of two mutant MVM capsids and compared their equilibrium dynamics with that of the wild-type MVM capsid. The results supported a previously suggested linkage between mechanical stiffening and impaired equilibrium dynamics of a virus particle. Cryo-EM is emerging as a powerful approach for simultaneously acquiring information on the atomic structure and local equilibrium dynamics of biomolecular complexes. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14519.map.gz | 49 MB | EMDB map data format | |
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Header (meta data) | emd-14519-v30.xml emd-14519.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_14519.png | 251.6 KB | ||
Others | emd_14519_additional_1.map.gz emd_14519_half_map_1.map.gz emd_14519_half_map_2.map.gz | 39.3 MB 39.5 MB 39.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14519 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14519 | HTTPS FTP |
-Related structure data
Related structure data | 7z5dMC 7z5eC 7z5fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14519.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | VP2-only capsid of wt MVM prototype strain p sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: VP2-only capsid of wt MVM prototype strain p unsharpened map
File | emd_14519_additional_1.map | ||||||||||||
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Annotation | VP2-only capsid of wt MVM prototype strain p unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: VP2-only capsid of wt MVM prototype strain p half map 1
File | emd_14519_half_map_1.map | ||||||||||||
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Annotation | VP2-only capsid of wt MVM prototype strain p half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: VP2-only capsid of wt MVM prototype strain p half map 2
File | emd_14519_half_map_2.map | ||||||||||||
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Annotation | VP2-only capsid of wt MVM prototype strain p half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Minute virus of mice
Entire | Name: Minute virus of mice |
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Components |
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-Supramolecule #1: Minute virus of mice
Supramolecule | Name: Minute virus of mice / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10794 / Sci species name: Minute virus of mice / Sci species strain: prototype / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Minute virus of mice / Strain: MVM prototype |
Molecular weight | Theoretical: 64.602469 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSDGTSQPDS GNAVHSAARV ERAADGPGGS GGGGSGGGGV GVSTGSYDNQ THYRFLGDGW VEITALATRL VHLNMPKSEN YCRIRVHNT TDTSVKGNMA KDDAHEQIWT PWSLVDANAW GVWLQPSDWQ YICNTMSQLN LVSLDQEIFN VVLKTVTEQD L GGQAIKIY ...String: MSDGTSQPDS GNAVHSAARV ERAADGPGGS GGGGSGGGGV GVSTGSYDNQ THYRFLGDGW VEITALATRL VHLNMPKSEN YCRIRVHNT TDTSVKGNMA KDDAHEQIWT PWSLVDANAW GVWLQPSDWQ YICNTMSQLN LVSLDQEIFN VVLKTVTEQD L GGQAIKIY NNDLTACMMV AVDSNNILPY TPAANSMETL GFYPWKPTIA SPYRYYFCVD RDLSVTYENQ EGTVEHNVMG TP KGMNSQF FTIENTQQIT LLRTGDEFAT GTYYFDTNPV KLTHTWQTNR QLGQPPLLST FPEADTDAGT LTAQGSRHGT TQM GVNWVS EAIRTRPAQV GFCQPHNDFE ASRAGPFAAP KVPADITQGV DKEANGSVRY SYGKQHGENW ASHGPAPERY TWDE TSFGS GRDTKDGFIQ SAPLVVPPPL NGILTNANPI GTKNDIHFSN VFNSYGPLTA FSHPSPVYPQ GQIWDKELDL EHKPR LHIT APFVCKNNAP GQMLVRLGPN LTDQYDPNGA TLSRIVTYGT FFWKGKLTMR AKLRANTTWN PVYQVSAEDN GNSYMS VTK WLPTATGNMQ SVPLITRPVA RNTY |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 36.6 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 997001 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 210854 |