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- EMDB-36408: The cryo-EM structure of dengue VLP and human monoclonal antibodi... -

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Basic information

Entry
Database: EMDB / ID: EMD-36408
TitleThe cryo-EM structure of dengue VLP and human monoclonal antibodies complex
Map data
Sample
  • Complex: Human monoclonal antibody and dengue VLP complex
    • Other: Human Monoclonal Antibody: K8b
Keywordshuman monoclonal antibodies / dengue VLP / cryo-EM / VIRUS LIKE PARTICLE / VIRUS
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsWu SR / Chao DY
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)110-2313-B-005-041; 110-2326-B-006 -001 -MY3 Taiwan
CitationJournal: Commun Biol / Year: 2024
Title: Antibodies from dengue patients with prior exposure to Japanese encephalitis virus are broadly neutralizing against Zika virus.
Authors: Gielenny M Salem / Jedhan Ucat Galula / Shang-Rung Wu / Jyung-Hurng Liu / Yen-Hsu Chen / Wen-Hung Wang / Sheng-Fan Wang / Cheng-Sheng Song / Fan-Chi Chen / Adrian B Abarientos / Guan-Wen ...Authors: Gielenny M Salem / Jedhan Ucat Galula / Shang-Rung Wu / Jyung-Hurng Liu / Yen-Hsu Chen / Wen-Hung Wang / Sheng-Fan Wang / Cheng-Sheng Song / Fan-Chi Chen / Adrian B Abarientos / Guan-Wen Chen / Cheng-I Wang / Day-Yu Chao /
Abstract: Exposure to multiple mosquito-borne flaviviruses within a lifetime is not uncommon; however, how sequential exposures to different flaviviruses shape the cross-reactive humoral response against an ...Exposure to multiple mosquito-borne flaviviruses within a lifetime is not uncommon; however, how sequential exposures to different flaviviruses shape the cross-reactive humoral response against an antigen from a different serocomplex has yet to be explored. Here, we report that dengue-infected individuals initially primed with the Japanese encephalitis virus (JEV) showed broad, highly neutralizing potencies against Zika virus (ZIKV). We also identified a rare class of ZIKV-cross-reactive human monoclonal antibodies with increased somatic hypermutation and broad neutralization against multiple flaviviruses. One huMAb, K8b, binds quaternary epitopes with heavy and light chains separately interacting with overlapping envelope protein dimer units spanning domains I, II, and III through cryo-electron microscopy and structure-based mutagenesis. JEV virus-like particle immunization in mice further confirmed that such cross-reactive antibodies, mainly IgG3 isotype, can be induced and proliferate through heterologous dengue virus (DENV) serotype 2 virus-like particle stimulation. Our findings highlight the role of prior immunity in JEV and DENV in shaping the breadth of humoral response and provide insights for future vaccination strategies in flavivirus-endemic countries.
History
DepositionJun 3, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36408.png

Downloads & links

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Map

FileDownload / File: emd_36408.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 220 pix.
= 220. Å		1 Å/pix.
x 220 pix.
= 220. Å		1 Å/pix.
x 220 pix.
= 220. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-2.7597609 - 4.577253
Average (Standard dev.)0.019678516 (±0.67830247)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-42-42-42
Dimensions220220220
Spacing220220220
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36408_half_map_1.map
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Half map: #1

Fileemd_36408_half_map_2.map
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Sample components

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Entire : Human monoclonal antibody and dengue VLP complex

EntireName: Human monoclonal antibody and dengue VLP complex
Components
  • Complex: Human monoclonal antibody and dengue VLP complex
    • Other: Human Monoclonal Antibody: K8b

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Supramolecule #1: Human monoclonal antibody and dengue VLP complex

SupramoleculeName: Human monoclonal antibody and dengue VLP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 600 KDa

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Macromolecule #1: Human Monoclonal Antibody: K8b

MacromoleculeName: Human Monoclonal Antibody: K8b / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVS HEDPEVKFNW YVDGVEVHNA ...String:
ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDKTHTCP PCPAPELLGG PSVFLFPPKP KDTLMISRTP EVTCVVVDVS HEDPEVKFNW YVDGVEVHNA KTKPREEQYN STYRVVSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSRDE LTKNQVSLTC LVKGFYPSDI AVEWESNGQP ENNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK
Recombinant expressionOrganism: Homo sapiens (human)

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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

Concentration1 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris-HCl
100.0 mMNaClNaCl
0.1 mMEDTAEDTA

Details: TNM buffer: 50 mM Tris-HCl, 100mM NaCl, 0.1 mM EDTA
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1000 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 86 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3
Details: Vitrification was carried out using standard procedure.
DetailsThe sample is heterogeneous in size

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Electron microscopy

MicroscopeJEOL 2100F
Specialist opticsPhase plate: OTHER / Spherical aberration corrector: Cs corrrector / Chromatic aberration corrector: Cs corrector / Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 35 eV / Details: Standard Procedure
DetailsPreliminary grid screening was performed manually
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Detector mode: COUNTING / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 3.0 µm / Calibrated magnification: 15000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 15000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2035
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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