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- PDB-9tx4: Mature MoMLV capsid hexamer 3-fold interface from capsid-like par... -

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Basic information

Entry
Database: PDB / ID: 9tx4
TitleMature MoMLV capsid hexamer 3-fold interface from capsid-like particles
ComponentsCapsid protein p30
KeywordsVIRAL PROTEIN / MLV / capsid / mature / CA / IP6 / retrovirus / hexamer / 3-fold axis / C3 / capsomer
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / viral genome integration into host DNA / protein-DNA complex / establishment of integrated proviral latency / host multivesicular body ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / viral genome integration into host DNA / protein-DNA complex / establishment of integrated proviral latency / host multivesicular body / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell cytoplasm / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / : / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesMoloney murine leukemia virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKlarhof, J.O. / Stacey, J.C.V. / Briggs, J.A.G. / James, L.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105181010 United Kingdom
Wellcome Trust200594/Z/16/Z United Kingdom
Wellcome Trust214344/A/18/Z United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Retroviruses use different IP binding mechanisms to alter the properties of their capsids.
Authors: J Ole Klarhof / Donna L Mallery / James C V Stacey / Davide Torre / Michaela Rumlova / Tomas Ruml / John A G Briggs / Leo C James /
Abstract: HIV-1 uses the metabolite inositol hexakisphosphate (IP) as a host factor to assemble its capsid, but whether this strategy is unique to lentiviruses or represents a common feature of retroviral ...HIV-1 uses the metabolite inositol hexakisphosphate (IP) as a host factor to assemble its capsid, but whether this strategy is unique to lentiviruses or represents a common feature of retroviral capsids remains unclear. Here we show that IP binding is conserved across diverse retroviruses but occurs through distinct capsid sites and mechanisms, and influences viral behaviour. In contrast to HIV-1, the beta-retrovirus Mason-Pfizer Monkey Virus (MPMV) and the gamma-retrovirus Murine Leukaemia Virus (MLV) bind IP at the threefold lattice interface between capsomers rather than within capsomer pores. Cryo-EM structures of core-like particles reveal that two lysine residues from each capsomer coordinate IP between either two discrete three-lysine rings (MPMV) or a single heterogeneous six-lysine ring (MLV). MPMV and MLV are largely insensitive to IP availability in producer cells, but this binding mode renders them highly dependent on IP6 in target cells - the opposite of the dependency pattern of HIV-1. The way in which retroviruses use IP to build their capsids alters their dependence on the metabolite at different stages of the replicative cycle and in key capsid behaviours, such as assembly and stability.
History
DepositionJan 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein p30
B: Capsid protein p30
C: Capsid protein p30


Theoretical massNumber of molelcules
Total (without water)91,9713
Polymers91,9713
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Capsid protein p30 / CA


Mass: 30657.123 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03355
Has protein modificationN

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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: MPMV Mature Capsid E26A (5mM IP6) / Type: COMPLEX / Details: Hexamer / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.03 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: C41 (DE3)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C41 (DE3)
Details of virusType: VIRION
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
12.5 mMinositol hexakisphosphateC6H18O24P61
250 mMTRIS hydrochlorideC4H11NO3HCl1
32 mMTCEPC9H15O6P1
SpecimenConc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: MPMV capsid-like particles assembled from recombinant capsid in 2.5mM IP6
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 96000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9.9particle selection
2EPU3image acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
10PHENIXmodel refinement
11cryoSPARC4.4.1initial Euler assignment
12cryoSPARC4.4.1final Euler assignment
13cryoSPARC4.4.1classification
14cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9098084
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150880 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation

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