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- EMDB-70931: CryoEM structure of stabilized dengue 3 virus envelope glycoprote... -

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Basic information

Entry
Database: EMDB / ID: EMD-70931
TitleCryoEM structure of stabilized dengue 3 virus envelope glycoprotein in complex with Fab of F25.S01
Map dataSharpened map of F25.S02 bound to DenV3 sE sc30 dimer
Sample
  • Complex: Complex of F25.S02 Fab bound to DenV3 sE sc30
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: F25.S02 Heavy chain
    • Protein or peptide: F25.S02 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsOrthoflavivirus / Dengue / IMMUNE SYSTEM
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region
Similarity search - Function
Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 ...Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / dengue virus type 3
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsHurlburt NK / Pancera M
Funding support1 items
OrganizationGrant numberCountry
Other privateFred Hutchinson Cancer Center
CitationJournal: Commun Biol / Year: 2026
Title: Structural basis for antibody cross-neutralization of Dengue and Zika viruses.
Authors: Nicholas K Hurlburt / Jay Lubow / Leslie Goo / Marie Pancera /
Abstract: Safe and effective vaccines against co-circulating mosquito-borne orthoflaviviruses such as Zika virus (ZikV) and the four serotypes of Dengue virus (DenV1-4) must elicit broadly neutralizing ...Safe and effective vaccines against co-circulating mosquito-borne orthoflaviviruses such as Zika virus (ZikV) and the four serotypes of Dengue virus (DenV1-4) must elicit broadly neutralizing antibodies (bnAbs) to prevent the risk of enhancement of infection by non-neutralizing antibodies. We recently discovered new orthoflavivirus-directed bnAbs, including F25.S02, which neutralizes DenV1-4 and ZikV with comparable or superior potency to the previously characterized E dimer epitope (EDE) bnAbs. Here, we used cryoEM and X-ray crystallography to understand the basis of cross-neutralization of F25.S02 at the molecular level. We obtained a ~ 4.2 Å cryoEM structure of F25.S02 Fab bound to a stabilized DenV3 soluble E protein dimer and a 2.3 Å crystal structure of F25.S02 Fab bound to ZikV soluble E protein dimer. Like previously described EDE1 bnAbs, the structural epitope of F25.S02 is at the E dimer interface, encompassing predominantly conserved regions in domain II, including the fusion loop. However, unlike EDE1 bnAbs, F25.S02 binding is almost entirely dependent on the heavy chain and is shifted slightly away from the dimer symmetry axis. Our findings emphasize the importance of this cross-neutralizing site of vulnerability for DenV and ZikV that can facilitate rational design of vaccines and therapeutics.
History
DepositionJun 2, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70931.png

Downloads & links

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Map

FileDownload / File: emd_70931.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of F25.S02 bound to DenV3 sE sc30 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 359.04 Å		1.12 Å/pix.
x 320 pix.
= 359.04 Å		1.12 Å/pix.
x 320 pix.
= 359.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.2393348 - 4.310036
Average (Standard dev.)0.0018739523 (±0.08489051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 359.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A of F25.S02 bound to DenV3 sE sc30 dimer

Fileemd_70931_half_map_1.map
AnnotationHalf-map A of F25.S02 bound to DenV3 sE sc30 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of F25.S02 bound to DenV3 sE sc30 dimer

Fileemd_70931_half_map_2.map
AnnotationHalf-map B of F25.S02 bound to DenV3 sE sc30 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of F25.S02 Fab bound to DenV3 sE sc30

EntireName: Complex of F25.S02 Fab bound to DenV3 sE sc30
Components
  • Complex: Complex of F25.S02 Fab bound to DenV3 sE sc30
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: F25.S02 Heavy chain
    • Protein or peptide: F25.S02 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of F25.S02 Fab bound to DenV3 sE sc30

SupramoleculeName: Complex of F25.S02 Fab bound to DenV3 sE sc30 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 3
Molecular weightTheoretical: 45.00132 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGKC VTVMMKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCDLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGKC VTVMMKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCDLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGC MHTALTGATE IQNSGGTSIW PGHLKCRLKM DKLELKGMSY AMCLNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDKALK INWYKKGSSG GSHH HHHHH H

UniProtKB: Genome polyprotein

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Macromolecule #2: F25.S02 Heavy chain

MacromoleculeName: F25.S02 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.57567 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (PCA)VQLVQSGAE VKKPGSSAKV SCKASGGTFS SYAISWVRQA PGQGLEWMGS IMPIFGTVNY AQKFQGRVTI TADEST STA YMELSRLRSE DTAVYFCARG WGGNYRSADL WIYFDLWGQG TLVTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVK DY FPEPVTVSWN ...String:
(PCA)VQLVQSGAE VKKPGSSAKV SCKASGGTFS SYAISWVRQA PGQGLEWMGS IMPIFGTVNY AQKFQGRVTI TADEST STA YMELSRLRSE DTAVYFCARG WGGNYRSADL WIYFDLWGQG TLVTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVK DY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CDKTHHHH H H

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Macromolecule #3: F25.S02 Light chain

MacromoleculeName: F25.S02 Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.023486 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPRSV SGSPGQSVTI SCTGTSSDVG GYKYVSWYQQ HPGKAPKLMI YDVTKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYAGSYTH VVFGGGTKLT VLGQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSALTQPRSV SGSPGQSVTI SCTGTSSDVG GYKYVSWYQQ HPGKAPKLMI YDVTKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYAGSYTH VVFGGGTKLT VLGQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7a3p

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111111
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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