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- EMDB-54561: RVFV Gn-Ferritin Nanoparticle -

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Basic information

Entry
Database: EMDB / ID: EMD-54561
TitleRVFV Gn-Ferritin Nanoparticle
Map data
Sample
  • Complex: Rift Valley fever virus Gn membrane glycoprotein fused to bullfrog-H. pylori ferritin nanoparticle
    • Other: Rift Valley fever virus Gn membrane glycoprotein
    • Other: Helicobacter pylori ferritin
KeywordsFerritin / Nanoparticle / Rift Valley fever virus / Gn membrane glycoprotein / VIRAL PROTEIN
Function / homology
Function and homology information


: / bacterial non-heme ferritin / host cell mitochondrial outer membrane / ferroxidase activity / host cell Golgi membrane / ferric iron binding / iron ion transport / ferrous iron binding / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane ...: / bacterial non-heme ferritin / host cell mitochondrial outer membrane / ferroxidase activity / host cell Golgi membrane / ferric iron binding / iron ion transport / ferrous iron binding / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion membrane / membrane / cytoplasm / cytosol
Similarity search - Function
Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / Ferritin, prokaryotic-type ...Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Envelopment polyprotein / Bacterial non-heme ferritin
Similarity search - Component
Biological speciesRift Valley fever virus / Helicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.76 Å
AuthorsRodrigues MQ
Funding support Portugal, 3 items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)PhD fellowship (DFA/BD/8167/2020) Portugal
Foundation for Science and Technology (FCT)Research Unit UID/04462: iNOVA4Health - Programme in Translational Medicine Portugal
Foundation for Science and Technology (FCT)Associate Laboratory LS4FUTURE (LA/P/0087/2020) Portugal
CitationJournal: Virol J / Year: 2026
Title: Ferritin nanoparticles displaying rift valley fever virus glycoprotein elicit potent dendritic cell activation in vitro.
Authors: Margarida Q Rodrigues / Inês Cardoso / Nádia Duarte / Paula M Alves / António Roldão /
Abstract: Rift Valley fever (RVF) is a mosquito-borne zoonosis of major concern for human and animal health, yet no licensed human vaccine exists. Here, we engineered a self-assembling nanoparticle vaccine ...Rift Valley fever (RVF) is a mosquito-borne zoonosis of major concern for human and animal health, yet no licensed human vaccine exists. Here, we engineered a self-assembling nanoparticle vaccine candidate by genetically fusing the RVF virus glycoprotein Gn to the N-terminus of a hybrid bacterial ferritin, generating nanoparticles that display 24 copies of Gn on their surface. Cryo-electron microscopy at 6 Å resolution confirmed ordered and symmetric presentation of the antigens, consistent with the structural models of ferritin and Gn. When incubated with human monocyte-derived dendritic cells, the Gn-ferritin nanoparticles were efficiently internalized and induced robust expression of maturation markers (e.g., CD54, CD83, CD86) and secretion of pro-inflammatory cytokines (e.g., IL-1β, IL-6, IL-12p40, TNF-α), in contrast to soluble Gn or ferritin controls. These findings demonstrate that ferritin nanoparticles provide a structurally defined and immunologically active platform for RVF virus antigen display, establishing a foundation for the development of safe and effective subunit vaccines against this emerging pathogen.
History
DepositionJul 26, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54561.png

Downloads & links

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Map

FileDownload / File: emd_54561.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 440 pix.
= 524.04 Å		1.19 Å/pix.
x 440 pix.
= 524.04 Å		1.19 Å/pix.
x 440 pix.
= 524.04 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.191 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00172
Minimum - Maximum-0.017098393 - 0.031182222
Average (Standard dev.)0.0010808614 (±0.0045385873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 524.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54561_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54561_half_map_2.map
Projections & Slices
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Sample components

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Entire : Rift Valley fever virus Gn membrane glycoprotein fused to bullfro...

EntireName: Rift Valley fever virus Gn membrane glycoprotein fused to bullfrog-H. pylori ferritin nanoparticle
Components
  • Complex: Rift Valley fever virus Gn membrane glycoprotein fused to bullfrog-H. pylori ferritin nanoparticle
    • Other: Rift Valley fever virus Gn membrane glycoprotein
    • Other: Helicobacter pylori ferritin

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Supramolecule #1: Rift Valley fever virus Gn membrane glycoprotein fused to bullfro...

SupramoleculeName: Rift Valley fever virus Gn membrane glycoprotein fused to bullfrog-H. pylori ferritin nanoparticle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Histidine tag followed by Rift Valley fever virus membrane glycoprotein Gn head domain sequence (res. 154-467, UniProt ID: P03518, with point mutations E276G, L329, and I444V), followed by a ...Details: Histidine tag followed by Rift Valley fever virus membrane glycoprotein Gn head domain sequence (res. 154-467, UniProt ID: P03518, with point mutations E276G, L329, and I444V), followed by a GS-linker (GGGGSGGGGS), and finally the bullfrog-Helicobacter pylori ferritin hybrid, composed of bullfrog (Rana catesbeiana) ferritin lower subunit (res. 2-9, PDB ID: 1RCC, with a point mutation N8Q) and H. pylori ferritin (res. 3-167, PDB ID: 3BVE, with point mutations I7E and N19Q). RVFV Gn-ferritin nanoparticles self assemble into 24-mer nanoparticles after recombinant expression of monomeric parts.
Source (natural)Organism: Rift Valley fever virus
Molecular weightTheoretical: 1.4 MDa

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Macromolecule #1: Rift Valley fever virus Gn membrane glycoprotein

MacromoleculeName: Rift Valley fever virus Gn membrane glycoprotein / type: other / ID: 1
Details: Histidine tag followed by Rift Valley fever virus membrane glycoprotein Gn head domain sequence (res. 154-467, UniProt ID: P03518, with point mutations E276G, L329, and I444V), followed by a ...Details: Histidine tag followed by Rift Valley fever virus membrane glycoprotein Gn head domain sequence (res. 154-467, UniProt ID: P03518, with point mutations E276G, L329, and I444V), followed by a GS-linker (GGGGSGGGGS), and finally the bullfrog-Helicobacter pylori ferritin hybrid, composed of bullfrog (Rana catesbeiana) ferritin lower subunit (res. 2-9, PDB ID: 1RCC, with a point mutation N8Q) and H. pylori ferritin (res. 3-167, PDB ID: 3BVE, with point mutations I7E and N19Q)
Classification: other
Source (natural)Organism: Rift Valley fever virus
SequenceString: HHHHHHEDPH LRNRPGKGHN YIDGMTQEDA TCKPVTYAGA CSSFDVLLEK GKFPLFQSYA HHRTLLEAVH DTIIAKADPP SCDLQSAHGN PCMKEKLVMK THCPNDYQSA HYLNNDGKMA SVKCPPKYEL TEDCNFCRQM TGASLKKGSY PLQDLFCQSS EDDGSKLKTK ...String:
HHHHHHEDPH LRNRPGKGHN YIDGMTQEDA TCKPVTYAGA CSSFDVLLEK GKFPLFQSYA HHRTLLEAVH DTIIAKADPP SCDLQSAHGN PCMKEKLVMK THCPNDYQSA HYLNNDGKMA SVKCPPKYEL TEDCNFCRQM TGASLKKGSY PLQDLFCQSS EDDGSKLKTK MKGVCEVGVQ ALKKCDGQLS TAHEVVPFAV FKNSKKVYLD KLDLKTEENL LPDSFVCFEH KGQYKGTMDS GQTKRELKSF DISQCPKIGG HGSKKCTGDA AFCSAYECTA QYANAYCSHA NGSGVVQIQV SGVWKKPLCV GYERVVVKRE GGGGSGGGGS ESQVRQQFSK DIEKLLNEQV NKEMQSSNLY MSMSSWCYTH SLDGAGLFLF DHAAEEYEHA KKLIIFLNEN NVPVQLTSIS APEHKFEGLT QIFQKAYEHE QHISESINNI VDHAIKSKDH ATFNFLQWYV AEQHEEEVLF KDILDKIELI GNENHGLYLA DQYVKGIAKS RKS

UniProtKB: Envelopment polyprotein
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #2: Helicobacter pylori ferritin

MacromoleculeName: Helicobacter pylori ferritin / type: other / ID: 2
Details: Histidine tag followed by Rift Valley fever virus membrane glycoprotein Gn head domain sequence (res. 154-467, UniProt ID: P03518, with point mutations E276G, L329, and I444V), followed by a ...Details: Histidine tag followed by Rift Valley fever virus membrane glycoprotein Gn head domain sequence (res. 154-467, UniProt ID: P03518, with point mutations E276G, L329, and I444V), followed by a GS-linker (GGGGSGGGGS), and finally the bullfrog-Helicobacter pylori ferritin hybrid, composed of bullfrog (Rana catesbeiana) ferritin lower subunit (res. 2-9, PDB ID: 1RCC, with a point mutation N8Q) and H. pylori ferritin (res. 3-167, PDB ID: 3BVE, with point mutations I7E and N19Q)
Classification: other
Source (natural)Organism: Helicobacter pylori (bacteria)
SequenceString: HHHHHHEDPH LRNRPGKGHN YIDGMTQEDA TCKPVTYAGA CSSFDVLLEK GKFPLFQSYA HHRTLLEAVH DTIIAKADPP SCDLQSAHGN PCMKEKLVMK THCPNDYQSA HYLNNDGKMA SVKCPPKYEL TEDCNFCRQM TGASLKKGSY PLQDLFCQSS EDDGSKLKTK ...String:
HHHHHHEDPH LRNRPGKGHN YIDGMTQEDA TCKPVTYAGA CSSFDVLLEK GKFPLFQSYA HHRTLLEAVH DTIIAKADPP SCDLQSAHGN PCMKEKLVMK THCPNDYQSA HYLNNDGKMA SVKCPPKYEL TEDCNFCRQM TGASLKKGSY PLQDLFCQSS EDDGSKLKTK MKGVCEVGVQ ALKKCDGQLS TAHEVVPFAV FKNSKKVYLD KLDLKTEENL LPDSFVCFEH KGQYKGTMDS GQTKRELKSF DISQCPKIGG HGSKKCTGDA AFCSAYECTA QYANAYCSHA NGSGVVQIQV SGVWKKPLCV GYERVVVKRE GGGGSGGGGS ESQVRQQFSK DIEKLLNEQV NKEMQSSNLY MSMSSWCYTH SLDGAGLFLF DHAAEEYEHA KKLIIFLNEN NVPVQLTSIS APEHKFEGLT QIFQKAYEHE QHISESINNI VDHAIKSKDH ATFNFLQWYV AEQHEEEVLF KDILDKIELI GNENHGLYLA DQYVKGIAKS RKS

UniProtKB: Bacterial non-heme ferritin
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 4 sec.
Details: Quantifoil R1.2/1.3 Cu 300-mesh grids were rendered hydrophilic using a Fischione 1020 plasma cleaner for 4 s.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Quantifoil R1.2/1.3 Cu 300-mesh grids were rendered hydrophilic using a Fischione 1020 plasma cleaner for 4 s. A sample at a concentration of 1 mg/mL was vitrified using a Vitrobot Mark IV ...Details: Quantifoil R1.2/1.3 Cu 300-mesh grids were rendered hydrophilic using a Fischione 1020 plasma cleaner for 4 s. A sample at a concentration of 1 mg/mL was vitrified using a Vitrobot Mark IV by applying 3.5 uL onto the freshly plasma-cleaned grid under controlled conditions (4C, 100% humidity, blot force 2, blot time 2.5-4 s) before being plunge-frozen in liquid ethane..

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4534 / Average electron dose: 60.0 e/Å2
Details: Image acquisition was performed with EPU 3.6; each image was composed of 40 individual frames using a pixel size of 1.191 A and a total exposure dose of 60 e/A^2. A total of 4,534 movie stacks were acquired.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

DetailsThe grids were then clipped and loaded into a Glacios 200 kV microscope and imaged using a Falcon 4i camera in EER format, with a dose rate of approximately 6 e/pixel/s. Image acquisition was performed with EPU 3.6; each image was composed of 40 individual frames using a pixel size of 1.191 A and a total exposure dose of 60 e/A^2
Particle selectionNumber selected: 616911
Details: 305 particles were manually picked from eight micrographs and subjected to 2D classification. Selected classes were subsequently used as templates to extract a total of 616,911 particles from 4,534 movies.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6)
Details: All movie stacks were imported into CryoSPARC v4.6.0 for image processing. Following motion correction and contrast transfer function (CTF) estimation, 305 particles were manually picked ...Details: All movie stacks were imported into CryoSPARC v4.6.0 for image processing. Following motion correction and contrast transfer function (CTF) estimation, 305 particles were manually picked from eight micrographs and subjected to 2D classification. Selected classes were subsequently used as templates to extract a total of 616,911 particles from 4,534 movies.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Four iterative rounds of 2D classification were performed, resulting in a final set of 47,705 particles, which were used for ab initio reconstruction with octahedral symmetry to generate the ...Details: Four iterative rounds of 2D classification were performed, resulting in a final set of 47,705 particles, which were used for ab initio reconstruction with octahedral symmetry to generate the initial model. A single round of 3D classification was then carried out, from which the most populated class, comprising 11,551 particles, was selected for further 3D refinement under octahedral symmetry.
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 11551
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 5 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. 4.6)

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