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- EMDB-36436: Cryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36436
TitleCryo-EM structure of dengue virus serotype 3 strain EHIE46200Y19 in complex with human antibody DENV-115 IgG at 4 deg C
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
      • Protein or peptide: Membrane protein
    • 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
Biological speciesDengue virus type 3 / Homo sapiens (human) / dengue virus type 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36436.png

Downloads & links

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Map

FileDownload / File: emd_36436.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.)
1.62 Å/pix.
x 512 pix.
= 830.464 Å		1.62 Å/pix.
x 512 pix.
= 830.464 Å		1.62 Å/pix.
x 512 pix.
= 830.464 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: 1.5
Minimum - Maximum-11.367404000000001 - 22.721962000000001
Average (Standard dev.)-0.000000000133642 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 830.464 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36436_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_36436_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_36436_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
      • Protein or peptide: Membrane protein
    • 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: Dengue virus type 3

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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

MacromoleculeName: Envelope protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 3
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

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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:
SVALAPHVGM GLDTRAQTWM SAEGAWRQIE KVETWAFRHP GFTILALFLA HYIGTSLTQK VVIFILLMLV TPSMT

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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 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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 70158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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