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- EMDB-56393: Mature MPMV capsid pentamer structure from capsid-like particles -

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Basic information

Entry
Database: EMDB / ID: EMD-56393
TitleMature MPMV capsid pentamer structure from capsid-like particles
Map data
Sample
  • Complex: MPMV Mature Capsid (5mM IP6)
    • Protein or peptide: Capsid protein p27
KeywordsMPMV / M-PMV / capsid / mature / CA / p27 / IP6 / retrovirus / pentamer / capsomer / VIRAL PROTEIN
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 speciesEscherichia coli (E. coli) / Mason-Pfizer monkey virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKlarhof JO / Stacey JCV / Briggs JAG / James LC
Funding support United Kingdom, 3 items
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, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56393.png

Downloads & links

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Map

FileDownload / File: emd_56393.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.75392324 - 1.3637925
Average (Standard dev.)0.0006057054 (±0.029259829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56393_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56393_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56393_half_map_2.map
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Sample components

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Entire : MPMV Mature Capsid (5mM IP6)

EntireName: MPMV Mature Capsid (5mM IP6)
Components
  • Complex: MPMV Mature Capsid (5mM IP6)
    • Protein or peptide: Capsid protein p27

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Supramolecule #1: MPMV Mature Capsid (5mM IP6)

SupramoleculeName: MPMV Mature Capsid (5mM IP6) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Pentamer
Source (natural)Organism: Escherichia coli (E. coli) / Strain: C41 (DE3)
Molecular weightTheoretical: 24 KDa

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Macromolecule #1: Capsid protein p27

MacromoleculeName: Capsid protein p27 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Mason-Pfizer monkey virus
Molecular weightTheoretical: 24.338018 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PVTETVDGQG QAWRHHNGFD FAVIKELKTA ASQYGATAPY TLAIVESVAD NWLTPTDWNT LVRAVLSGGD HLLWKSEFFE NCRDTAKRN QQAGNGWDFD MLTGSGNYSS TDAQMQYDPG LFAQIQAAAT KAWRKLPVKG DPGASLTGVK QGPDEPFADF V HRLITTAG ...String:
PVTETVDGQG QAWRHHNGFD FAVIKELKTA ASQYGATAPY TLAIVESVAD NWLTPTDWNT LVRAVLSGGD HLLWKSEFFE NCRDTAKRN QQAGNGWDFD MLTGSGNYSS TDAQMQYDPG LFAQIQAAAT KAWRKLPVKG DPGASLTGVK QGPDEPFADF V HRLITTAG RIFGSAEAGV DYVKQLAYEN ANPACQAAIR PYRKKTDLTG YIRLCSDIGP SYQQ

UniProtKB: Gag-Pro-Pol 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

Concentration12.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
5.0 mMC6H18O24P6inositol hexakisphosphate
50.0 mMC4H11NO3HClTRIS hydrochloride
2.0 mMC9H15O6PTCEP
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMPMV capsid-like particles assembled from recombinant capsid in 5mM IP6

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2876773
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 125837
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Target criteria: Cross-correlation
Output model

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

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