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- EMDB-14520: VP2-only capsid of MVM D263A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-14520
TitleVP2-only capsid of MVM D263A mutant
Map dataVP2-only capsid of MVM D263A sharpened map
Sample
  • Virus: Minute virus of mice
    • Protein or peptide: Capsid protein VP1
KeywordsCapsid / MVM / VLP / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / 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
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesMinute virus of mice
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLuque D / Ortega-Esteban A / Valbuena A / Vilas JL / Rodriguez-Huete A / Mateu MG / Caston JR
Funding support Spain, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-113287RB-I00 Spain
Autonomous Community of MadridP2018/NMT-4389 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-096635-B-100 Spain
CitationJournal: 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
DepositionMar 9, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14520.png

Downloads & links

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Map

FileDownload / File: emd_14520.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVP2-only capsid of MVM D263A sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1941109 - 1.2823766
Average (Standard dev.)0.0010761553 (±0.10774322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 328.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: VP2-only capsid of MVM D263A unsharpened map

Fileemd_14520_additional_1.map
AnnotationVP2-only capsid of MVM D263A unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VP2-only capsid of MVM D263A half map 2

Fileemd_14520_half_map_1.map
AnnotationVP2-only capsid of MVM D263A half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VP2-only capsid of MVM D263A half map 1

Fileemd_14520_half_map_2.map
AnnotationVP2-only capsid of MVM D263A half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Minute virus of mice

EntireName: Minute virus of mice
Components
  • Virus: Minute virus of mice
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Minute virus of mice

SupramoleculeName: 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

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Minute virus of mice / Strain: MVM prototype
Molecular weightTheoretical: 64.558461 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 LLRTGAEFAT 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

UniProtKB: Capsid protein VP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 36.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 941403
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1z14

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 458002
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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