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- PDB-9txa: Mature MPMV capsid pentamer structure from capsid-like particles -

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Basic information

Entry
Database: PDB / ID: 9txa
TitleMature MPMV capsid pentamer structure from capsid-like particles
ComponentsCapsid protein p27
KeywordsVIRAL PROTEIN / MPMV / M-PMV / capsid / mature / CA / p27 / IP6 / retrovirus / pentamer / capsomer
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA polymerase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity ...dUTP diphosphatase / dUTP diphosphatase activity / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA polymerase activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / 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 / viral translational frameshifting / symbiont entry into host cell / proteolysis / DNA binding / RNA binding / zinc ion binding
Similarity search - Function
: / ERVK-8-like, RNaseH-like domain / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / glycine rich nucleic binding domain / G-patch domain ...: / ERVK-8-like, RNaseH-like domain / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / glycine rich nucleic binding domain / G-patch domain / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / gag protein p24 N-terminal domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase-like, N-terminal / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retrovirus capsid, C-terminal / Retroviral matrix protein / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, N-terminal / zinc finger / 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
Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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

Downloads & links

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Assembly

Deposited unit
A: Capsid protein p27
B: Capsid protein p27
C: Capsid protein p27
D: Capsid protein p27
E: Capsid protein p27
F: Capsid protein p27
G: Capsid protein p27
H: Capsid protein p27
I: Capsid protein p27
J: Capsid protein p27
K: Capsid protein p27
L: Capsid protein p27
M: Capsid protein p27
N: Capsid protein p27
O: Capsid protein p27


Theoretical massNumber of molelcules
Total (without water)365,07015
Polymers365,07015
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 p27


Mass: 24338.018 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag-pro-pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P07572
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: MPMV Mature Capsid (5mM IP6) / Type: COMPLEX / Details: Pentamer / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.024 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
15 mMinositol hexakisphosphateC6H18O24P61
250 mMTRIS hydrochlorideC4H11NO3HCl1
32 mMTCEPC9H15O6P1
SpecimenConc.: 12.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: MPMV capsid-like particles assembled from recombinant capsid in 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
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstruction
13Cootmodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2876773
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125837 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation

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