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- EMDB-36434: Cryo-EM structure of the small tail club shape particle of dengue... -

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Basic information

Entry
Database: EMDB / ID: EMD-36434
TitleCryo-EM structure of the small tail club shape particle of dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C
Map datapostprocessed map
Sample
  • Complex: Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C
    • Complex: Dengue virus serotype 3 strain CH53489
      • Protein or peptide: Polyprotein (Fragment)
    • Complex: Human antibody DENV-290 Fab (heavy and light chain)
      • Protein or peptide: Human antibody DENV-290 heavy chain
      • Protein or peptide: Human antibody DENV-290 light chain
Keywordsdengue virus / human antibody / dengue-antibody structure / virus / VIRUS-IMMUNE SYSTEM complex
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 / membrane
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 speciesDengue virus type 3 / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 9.8 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_36434.png

Downloads & links

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Map

FileDownload / File: emd_36434.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 684. Å		1.71 Å/pix.
x 400 pix.
= 684. Å		1.71 Å/pix.
x 400 pix.
= 684. 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: 3.5
Minimum - Maximum-4.9715486 - 11.100811999999999
Average (Standard dev.)0.000000001855711 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 684.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36434_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_36434_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_36434_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

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 CH53489 in complex with human anti...

EntireName: Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C
Components
  • Complex: Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C
    • Complex: Dengue virus serotype 3 strain CH53489
      • Protein or peptide: Polyprotein (Fragment)
    • Complex: Human antibody DENV-290 Fab (heavy and light chain)
      • Protein or peptide: Human antibody DENV-290 heavy chain
      • Protein or peptide: Human antibody DENV-290 light chain

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Supramolecule #1: Dengue virus serotype 3 strain CH53489 in complex with human anti...

SupramoleculeName: Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 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 CH53489

SupramoleculeName: Dengue virus serotype 3 strain CH53489 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Dengue virus type 3

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Supramolecule #3: Human antibody DENV-290 Fab (heavy and light chain)

SupramoleculeName: Human antibody DENV-290 Fab (heavy and light chain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polyprotein (Fragment)

MacromoleculeName: Polyprotein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus type 3
Molecular weightTheoretical: 53.73066 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQNSGGTSIF AGHLKCRLKM DKLELKGMSY AMCLNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDKALK INWYKKGSSI GKMF EATAR GARRMAILGD TAWDFGSVGG VLNSLGKMVH QIFGSAYTAL FSGVSWIMKI GIGVLLTWIG LNSKNTSMSF SCIAI GIIT LYLGAVVQA

UniProtKB: Genome polyprotein

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Macromolecule #2: Human antibody DENV-290 heavy chain

MacromoleculeName: Human antibody DENV-290 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.495959 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVELVESGGD VVQPGKSLRL SCAASGFTFT NYAMHWLRQA PGKGLEWVAV ISSDVNDKYY ADSVKGRFTI SRDNSKNTLY LQMNSLTPE DTAVYYCARE QAVGTNPWAF DYWGQGTLVT VSS

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Macromolecule #3: Human antibody DENV-290 light chain

MacromoleculeName: Human antibody DENV-290 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.381966 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
HIVMTQSPLS LSVTPGQPAS ISCKSSQISS WGSDGKTYLY WYLQKPGQSP QLLIYEVSSR FSGVSDRFSG SGSGTDFTLK ISRVQAEDV GLYYCMQGLH LPLTFGQGTR LEIK

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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-290 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 18.29 Å
Applied symmetry - Helical parameters - Δ&Phi: 102.22 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 12156
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

Initial model
PDB IDChain

3j6s

source_name: PDB, initial_model_type: experimental model

3ztj

source_name: PDB, initial_model_type: experimental model

5chn

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8jn6:
Cryo-EM structure of the small tail club shape particle of dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C

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