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- EMDB-48335: CAEV CA Hexamer Assembled via Liposome Templating -

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Basic information

Entry
Database: EMDB / ID: EMD-48335
TitleCAEV CA Hexamer Assembled via Liposome Templating
Map dataEM Map of CAEV CA Hexamer solved via liposome templating.
SampleCaprine arthritis encephalitis virus strain Cork != Caprine arthritis encephalitis virus

Caprine arthritis encephalitis virus strain Cork

  • Virus: Caprine arthritis encephalitis virus
    • Protein or peptide: Capsid protein p25
KeywordsCAEV / Capsid / Hexamer / Viral Protein
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral capsid / nucleic acid binding / 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 speciesCaprine arthritis encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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_48335.png

Downloads & links

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Map

FileDownload / File: emd_48335.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM Map of CAEV CA Hexamer solved via liposome templating.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 400 pix.
= 212. Å		0.53 Å/pix.
x 400 pix.
= 212. Å		0.53 Å/pix.
x 400 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.53 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0152
Minimum - Maximum-0.031010827 - 0.07068935
Average (Standard dev.)0.00036139748 (±0.0034212337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48335_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 CAEV CA Hexamer solved via liposome templating.

Fileemd_48335_half_map_1.map
AnnotationEM Half Map A of CAEV CA Hexamer 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 CAEV CA Hexamer solved via liposome templating.

Fileemd_48335_half_map_2.map
AnnotationEM Half Map B of CAEV CA Hexamer 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 : Caprine arthritis encephalitis virus strain Cork

EntireName: Caprine arthritis encephalitis virus strain Cork
Components
  • Virus: Caprine arthritis encephalitis virus
    • Protein or peptide: Capsid protein p25

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Supramolecule #1: Caprine arthritis encephalitis virus

SupramoleculeName: Caprine arthritis encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11661 / Sci species name: Caprine arthritis encephalitis virus / Sci species strain: strain Cork / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Capra hircus (goat)

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Macromolecule #1: Capsid protein p25

MacromoleculeName: Capsid protein p25 / type: protein_or_peptide / ID: 1 / Details: CAEV CA with C-terminal His tag. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caprine arthritis encephalitis virus / Strain: Cork
Molecular weightTheoretical: 25.625027 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PIVVQAAGGR SWKAVDSVMF QQLQTVAMQH GLVSEDFERQ LAYYATTWTS KDILEVLAMM PGNRAQKELI QGKLNEEAER WRRNNPPPP AGGGLTVDQI MGVGQTNQAA AQANMDQARQ ICLQWVINAL RAVRHMAHRP GNPMLVKQKT NEPYEDFAAR L LEAIDAEP ...String:
PIVVQAAGGR SWKAVDSVMF QQLQTVAMQH GLVSEDFERQ LAYYATTWTS KDILEVLAMM PGNRAQKELI QGKLNEEAER WRRNNPPPP AGGGLTVDQI MGVGQTNQAA AQANMDQARQ ICLQWVINAL RAVRHMAHRP GNPMLVKQKT NEPYEDFAAR L LEAIDAEP VTQPIKDYLK LTLSYTNASA DCQKQMDRTL GQRVQQASVE EKMQACRDVG SEGFHHHHHH

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
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: OTHER
Details: HIV-1 CA Hexamer (EMDB 3465) 40 angstrom low pass filtered model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 699313
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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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
Output model

PDB-9mkr:
CAEV CA Hexamer Assembled via Liposome Templating

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