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- EMDB-48334: MVV CA Pentamer assembled via liposome templating -

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Basic information

Entry
Database: EMDB / ID: EMD-48334
TitleMVV CA Pentamer assembled via liposome templating
Map dataEM Map of MVV CA Pentamer solved via liposome templating.
Sample
  • Virus: Visna-maedi virus
    • Protein or peptide: Capsid protein p25
KeywordsMVV / Capsid / Pentamer / Viral Protein
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral capsid / nucleic acid binding / viral translational frameshifting / zinc ion binding
Similarity search - Function
: / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesVisna-maedi virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsArizaga F / Freniere C / Xiong Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI116313 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32GM008283 United States
CitationJournal: J Am Chem Soc / Year: 2025
Title: Exploring the Structural Divergence of HIV and SRLV Lentiviral Capsids.
Authors: Fidel Arizaga / Christian Freniere / Juan S Rey / Matthew Cook / Chunxiang Wu / Juan R Perilla / Yong Xiong /
Abstract: Lentiviruses require a mature capsid to package and traffic their viral genome for successful infection and propagation. Although the HIV-1 capsid structure has been extensively studied, structural ...Lentiviruses require a mature capsid to package and traffic their viral genome for successful infection and propagation. Although the HIV-1 capsid structure has been extensively studied, structural information is lacking for other lentiviral capsids, limiting our understanding. Using cryo-electron microscopy (cryo-EM) and a liposome-templating system, we assembled capsid-like particles (CLPs) and resolved capsid protein (CA) pentamer and hexamer lattice structures from the two major phylogenetic groups of small ruminant lentiviruses (SRLVs). These structures exhibit an overall lattice organization like HIV-1 but differ in key characteristics, notably the absence of inositol hexakisphosphate (IP6) in the SRLV CA lattice─a critical factor for HIV-1 capsid assembly and function. Additionally, SRLV CA pentamers show a unique N-terminal domain orientation, providing insights into SRLV capsid assembly mechanisms. These observations, together with our molecular dynamics (MD) simulation, results suggest a possible mechanism for importing deoxynucleotide triphosphate (dNTP) molecules into SRLV capsids. Furthermore, key regions of host factor interaction, such as the CypA binding motifs, have diverged in the SRLV CA assemblies. Our results contribute to understanding the SRLV lentiviral capsids which may facilitate structure-based inhibitor design strategies.
History
DepositionDec 18, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48334.png

Downloads & links

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Map

FileDownload / File: emd_48334.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM Map of MVV CA Pentamer solved via liposome templating.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 260 pix.
= 275.6 Å		1.06 Å/pix.
x 260 pix.
= 275.6 Å		1.06 Å/pix.
x 260 pix.
= 275.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0294
Minimum - Maximum-0.101127565 - 0.23347451
Average (Standard dev.)-0.008986156 (±0.02223481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 275.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48334_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM Half Map A of MVV CA Pentamer solved via liposome templating.

Fileemd_48334_half_map_1.map
AnnotationEM Half Map A of MVV CA Pentamer solved via liposome templating.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM Half Map B of MVV CA Pentamer solved via liposome templating.

Fileemd_48334_half_map_2.map
AnnotationEM Half Map B of MVV CA Pentamer solved via liposome templating.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Visna-maedi virus

EntireName: Visna-maedi virus
Components
  • Virus: Visna-maedi virus
    • Protein or peptide: Capsid protein p25

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Supramolecule #1: Visna-maedi virus

SupramoleculeName: Visna-maedi virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2169971 / Sci species name: Visna-maedi virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Ovis aries (sheep)

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Macromolecule #1: Capsid protein p25

MacromoleculeName: Capsid protein p25 / type: protein_or_peptide / ID: 1 / Details: MVV CA with C-terminal His tag with GSS linker. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Visna-maedi virus
Molecular weightTheoretical: 25.882219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVNLQAGGR SWKAVESVVF QQLQTVAMQH GLVSEDFERQ LAYYATTWTS KDILEVLAMM PGNRAQKELI QGKLNEEAER WVRQNPPGP NVLTVDQIMG VGQTNQQASQ ANMDQARQIC LQWVITALRS VRHMSHRPGN PMLVKQKNTE SYEDFIARLL E AIDAEPVT ...String:
PIVNLQAGGR SWKAVESVVF QQLQTVAMQH GLVSEDFERQ LAYYATTWTS KDILEVLAMM PGNRAQKELI QGKLNEEAER WVRQNPPGP NVLTVDQIMG VGQTNQQASQ ANMDQARQIC LQWVITALRS VRHMSHRPGN PMLVKQKNTE SYEDFIARLL E AIDAEPVT DPIKTYLKVT LSYTNASTDC QKQMDRTLGT RVQQATVEEK MQACRDVGSE GFGSSHHHHH H

UniProtKB: Gag polyprotein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.6.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: Used ModelAngelo to create an initial model for the solved density.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.1) / Number images used: 239010
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.6.1)
FSC plot (resolution estimation)

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