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

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Basic information

Entry
Database: PDB / ID: 9mkr
TitleCAEV CA Hexamer Assembled via Liposome Templating
ComponentsCapsid protein p25
KeywordsVIRAL PROTEIN / CAEV / Capsid / Hexamer
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsArizaga, F. / Freniere, C. / Xiong, Y.
Funding support United States, 3items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p25


Theoretical massNumber of molelcules
Total (without water)25,6251
Polymers25,6251
Non-polymers00
Water00
1
A: Capsid protein p25
x 6


Theoretical massNumber of molelcules
Total (without water)153,7506
Polymers153,7506
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Capsid protein p25


Mass: 25625.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CAEV CA with C-terminal His tag. / Source: (gene. exp.) Caprine arthritis encephalitis virus / Strain: Cork / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: P33458
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Caprine arthritis encephalitis virus strain Cork / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Caprine arthritis encephalitis virus / Strain: strain Cork
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pET28a
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Capra hircus
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARCv4.6.1CTF correction
9Cootmodel refinement
10cryoSPARCv4.6.1initial Euler assignment
11cryoSPARCv4.6.1final Euler assignment
13cryoSPARCv43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 699313 / Symmetry type: POINT
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model

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