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- EMDB-36429: Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36429
TitleCryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C (subparticle LLR-LRR)
Map datapostprocessed map
Sample
  • Complex: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C
    • Complex: Dengue virus serotype 3 strain EHIE46200Y19
      • Protein or peptide: Envelope protein (Fragment)
      • Protein or peptide: Polyprotein
    • Complex: Human antibody DENV-115 IgG (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
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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain ...Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesAedes albopictus (Asian tiger mosquito) / Homo sapiens (human) / Dengue virus type 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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: To Be Published
Title: Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants
Authors: Fibriansah G / Ng TS / Lim XN / Shebanova A / Ng LC / Tan SL / Tan AWK / Shi J / Crowe JE / Lok SM
History
DepositionJun 6, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36429.png

Downloads & links

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Map

FileDownload / File: emd_36429.map.gz / Format: CCP4 / Size: 34.3 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.)
1.62 Å/pix.
x 208 pix.
= 337.376 Å		1.62 Å/pix.
x 208 pix.
= 337.376 Å		1.62 Å/pix.
x 208 pix.
= 337.376 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.622 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-10.797848999999999 - 17.681522000000001
Average (Standard dev.)-0.000000000686364 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 337.376 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36429_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_36429_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_36429_half_map_2.map
Annotationhalf map 2
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 EHIE46200Y19 in complex with human...

EntireName: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C
Components
  • Complex: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C
    • Complex: Dengue virus serotype 3 strain EHIE46200Y19
      • Protein or peptide: Envelope protein (Fragment)
      • Protein or peptide: Polyprotein
    • Complex: Human antibody DENV-115 IgG (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 EHIE46200Y19 in complex with human...

SupramoleculeName: Dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Dengue virus serotype 3 strain EHIE46200Y19

SupramoleculeName: Dengue virus serotype 3 strain EHIE46200Y19 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Aedes albopictus (Asian tiger mosquito)

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

SupramoleculeName: Human antibody DENV-115 IgG (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 (Fragment)

MacromoleculeName: Envelope protein (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus type 3
Molecular weightTheoretical: 53.731734 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNVTT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLELIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNVTT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLELIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNKKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQTSGGTSIF AGHLKCRLKM DKLELKGMSY AMCSNAFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEELVNIE AEPPFGESNI IIGIGDKALR INWYKKGSSI GKMF EATAR GARRMAILGD TAWDFGSVGG VLNSLGKMVH QIFGSAYTAL FSGVSWIMKI GIGVLLTWIG LNSKNTSMSF SCIVI GIIT LYLGAVVQA

UniProtKB: Genome polyprotein

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Macromolecule #2: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus type 3
Molecular weightTheoretical: 8.365854 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
SVALAPHVGM GLDTRAQTWM SAEGAWRQIE KVETWAFRHP GFTILALFLA HYIGTSLTQK VVIFILLMLV TPSMT

UniProtKB: Genome polyprotein

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.607289 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGAPVKV SCEASGYTFT DYFIHWVRQA PGQGLEWMGW INPISGGTNY HPRFHGGVTM TRDTSMKVAY MELKRLTSD DTAVYFCARG RDFRGGYSQL DYWGQGTLVT VSS

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.49662 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGGSSNIA INTVNWYQQV PGTAPKLLMY SNNQRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC ATWDDSLKDV LFGGGTKLTV L

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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 IgG 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 22.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.6000000000000005 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

5933

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 181866
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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

5ifa

source_name: PDB, initial_model_type: experimental model

6qb6

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

PDB-8jn1:
Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C (subparticle LLR-LRR)

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