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- EMDB-36438: Cryo-EM structure of dengue virus serotype 3 strain 863DK in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-36438
TitleCryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg C
Map datapostprocessed map
Sample
  • Complex: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg C
    • Complex: Dengue virus serotype 3 strain 863DK
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane protein
    • Complex: Human antibody DENV-115 Fab (heavy and light chain)
      • Protein or peptide: Human antibody DENV-115 heavy chain
      • Protein or peptide: Human antibody DENV-115 light chain
Keywordsdengue virus / human antibody / dengue-antibody structure / virus
Biological speciesDengue virus type 3 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsFibriansah G / Ng TS / Tan AWK / Shi J / Lok SM
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
CitationJournal: Nat Commun / Year: 2025
Title: Ultrapotent human antibodies lock E protein dimers central region of diverse DENV3 morphological variants.
Authors: Guntur Fibriansah / Thiam-Seng Ng / Xin-Ni Lim / Anastasia Shebanova / Lee Ching Ng / Song Ling Tan / Aaron W K Tan / Jian Shi / James E Crowe / Shee-Mei Lok /
Abstract: Dengue virus (DENV) consists of four serotypes (DENV1-4). Current vaccines induce differing levels of immune response against the four serotypes, that might prime recipients to develop severe disease ...Dengue virus (DENV) consists of four serotypes (DENV1-4). Current vaccines induce differing levels of immune response against the four serotypes, that might prime recipients to develop severe disease in subsequent infections. Several DENV tetravalent vaccine clinical trials suggested an increased incidence in severe DENV3 cases, suggesting a need to develop DENV3 therapeutics. Human monoclonal antibodies (HMAbs) DENV-290 and DENV-115 are ultrapotent against diverse DENV3 strains with differing particle morphologies. They mainly neutralize by inhibition of virus attachment to cells. CryoEM structures of Fabs complexed with differing DENV3 morphological variants show their Fabs binding across two E protein protomers at the center of the E dimer. This new class of E protein dimer binding antibodies is named EDE-C. The cryoEM structures also show how IgGs engage the DENV particles. Results define the structural and molecular basis for the ultrapotent activity of EDE-C antibodies.
History
DepositionJun 6, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36438.png

Downloads & links

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Map

FileDownload / File: emd_36438.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 512 pix.
= 875.52 Å		1.71 Å/pix.
x 512 pix.
= 875.52 Å		1.71 Å/pix.
x 512 pix.
= 875.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-4.9851775 - 13.453659999999999
Average (Standard dev.)-0.000000003759936 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 875.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36438_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_36438_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_36438_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dengue virus serotype 3 strain 863DK in complex with human antibo...

EntireName: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg C
Components
  • Complex: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg C
    • Complex: Dengue virus serotype 3 strain 863DK
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane protein
    • Complex: Human antibody DENV-115 Fab (heavy and light chain)
      • Protein or peptide: Human antibody DENV-115 heavy chain
      • Protein or peptide: Human antibody DENV-115 light chain

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Supramolecule #1: Dengue virus serotype 3 strain 863DK in complex with human antibo...

SupramoleculeName: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Dengue virus serotype 3 strain 863DK

SupramoleculeName: Dengue virus serotype 3 strain 863DK / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Dengue virus type 3

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Supramolecule #3: Human antibody DENV-115 Fab (heavy and light chain)

SupramoleculeName: Human antibody DENV-115 Fab (heavy and light chain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope protein

MacromoleculeName: Envelope protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus type 3
SequenceString: mrcvgvgnrd fveglsgat w vdvvlehg gc vttmakn kpt ldielq ktea tqlat lrklc iegk itnitt dsr cptqgea vl peeqdqny v ckhtyvdrg wgngcglfgk gslvtcakf q clepiegk vv qyenlky tvi itvhtg dqhq vgnet ...String:
mrcvgvgnrd fveglsgat w vdvvlehg gc vttmakn kpt ldielq ktea tqlat lrklc iegk itnitt dsr cptqgea vl peeqdqny v ckhtyvdrg wgngcglfgk gslvtcakf q clepiegk vv qyenlky tvi itvhtg dqhq vgnet qgvta eitp qastte ail peygtlg le csprtgld f nemilltmk nkawmvhrqw ffdlplpwa s gattetpt wn rkellvt fkn ahakkq evvv lgsqe gamht altg ateiqn sgg tsifagh lk crlkmdkl e lkgmsyamc tntfvlkkev setqhgtil i kveykged ap ckipfst edg qgkahn grli tanpv vtkke epvn ieaepp fge snivigi gd nalkinwy k kgssigkmf eatargarrm ailgdtawd f gsvggvln sl gkmvhqi fgs aytalf sgvs wvmki gigvl ltwi glnskn tsm sfsciai gi itlylgav v qa

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Macromolecule #2: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus type 3
SequenceString:
svala phvg mgldtr tqt wmsaega wr qvekvetw a lrhpgftil alflahyigt sltqkvvif i llmlvtps mt

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Macromolecule #3: Human antibody DENV-115 heavy chain

MacromoleculeName: Human antibody DENV-115 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGAPVKV SCEASGYTFT DYFIHWVRQA PGQGLEWMGW INPISGGTNY HPRFHGGVTM TRDTSMKVAY MELKRLTSDD TAVYFCARGR DFRGGYSQLD YWGQGTLVTV SS

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Macromolecule #4: Human antibody DENV-115 light chain

MacromoleculeName: Human antibody DENV-115 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGGSSNIA INTVNWYQQV PGTAPKLLMY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYCA TWDDSLKDVL FGGGTKLTVL

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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: 8
Details: NTE buffer (12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA)
VitrificationCryogen name: ETHANE
DetailsThe purified virus was mixed with DENV-115 Fab at a molar ratio of 1.5 Fab for every E-protein and then the mixture was incubated at 4 deg C for 30 min. The complex was further incubated at 37 deg C for 30 min, and then incubated at 4 deg C for another 2 h

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 18.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

5933

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 27447
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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