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- EMDB-56388: Mature MoMLV capsid hexamer structure from capsid-like particles -

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Basic information

Entry
Database: EMDB / ID: EMD-56388
TitleMature MoMLV capsid hexamer structure from capsid-like particles
Map data
Sample
  • Complex: MPMV Mature Capsid E26A (5mM IP6)
    • Protein or peptide: Capsid protein p30
KeywordsMLV / capsid / mature / CA / IP6 / retrovirus / hexamer / capsomer / VIRAL PROTEIN
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 speciesEscherichia coli (E. coli) / Moloney murine leukemia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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_56388.png

Downloads & links

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Map

FileDownload / File: emd_56388.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.59203297 - 1.013344
Average (Standard dev.)0.0002484373 (±0.019987253)
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_56388_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56388_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56388_half_map_2.map
Projections & Slices
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Sample components

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Entire : MPMV Mature Capsid E26A (5mM IP6)

EntireName: MPMV Mature Capsid E26A (5mM IP6)
Components
  • Complex: MPMV Mature Capsid E26A (5mM IP6)
    • Protein or peptide: Capsid protein p30

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Supramolecule #1: MPMV Mature Capsid E26A (5mM IP6)

SupramoleculeName: MPMV Mature Capsid E26A (5mM IP6) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Hexamer
Source (natural)Organism: Escherichia coli (E. coli) / Strain: C41 (DE3)
Molecular weightTheoretical: 30 KDa

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Macromolecule #1: Capsid protein p30

MacromoleculeName: Capsid protein p30 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Moloney murine leukemia virus
Molecular weightTheoretical: 30.657123 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PLRAGGNGQL QYWPFSSSDL YNWKNNNPSF SEDPGKLTAL IESVLITHQP TWDDCQQLLG TLLTGEEKQR VLLEARKAVR GDDGRPTQL PNEVDAAFPL ERPDWDYTTQ AGRNHLVHYR QLLLAGLQNA GRSPTNLAKV KGITQGPNES PSAFLERLKE A YRRYTPYD ...String:
PLRAGGNGQL QYWPFSSSDL YNWKNNNPSF SEDPGKLTAL IESVLITHQP TWDDCQQLLG TLLTGEEKQR VLLEARKAVR GDDGRPTQL PNEVDAAFPL ERPDWDYTTQ AGRNHLVHYR QLLLAGLQNA GRSPTNLAKV KGITQGPNES PSAFLERLKE A YRRYTPYD PEDPGQETNV SMSFIWQSAP DIGRKLERLE DLKNKTLGDL VREAEKIFNK RETPEEREER IRRETEEKEE RR RTEDEQK EKERDRRRHR EMSKLL

UniProtKB: Gag-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

Concentration15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
2.5 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMPMV capsid-like particles assembled from recombinant capsid in 2.5mM 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: 9098084
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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 86595
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-9tx5:
Mature MoMLV capsid hexamer structure from capsid-like particles

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