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- EMDB-36439: Cryo-EM structure of dengue virus serotype 3 strain 863DK in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-36439
TitleCryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C
Map datapostprocessed map
Sample
  • Complex: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C
    • Complex: Dengue virus serotype 3 strain 863DK
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane protein
    • 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
Biological speciesDengue virus type 3 / Homo sapiens (human) / Aedes albopictus (Asian tiger mosquito)
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-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36439.png

Downloads & links

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Map

FileDownload / File: emd_36439.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-7.396718 - 18.475930000000002
Average (Standard dev.)0.000000007214275 (±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_36439_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_36439_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_36439_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 863DK in complex with human antibo...

EntireName: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C
Components
  • Complex: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 deg C
    • Complex: Dengue virus serotype 3 strain 863DK
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane protein
    • 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 863DK in complex with human antibo...

SupramoleculeName: Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 4 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-290 Fab (heavy and light chain)

SupramoleculeName: Human antibody DENV-290 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: Aedes albopictus (Asian tiger mosquito)
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA VLPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLEPIEGKV VQYENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGGC VTTMAKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA VLPEEQDQN YVCKHTYVDR GWGNGCGLFG KGSLVTCAKF QCLEPIEGKV VQYENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST TEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW ASGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGA MHTALTGATE IQNSGGTSIF AGHLKCRLKM DKLELKGMSY AMCTNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDNALK INWYKKGSSI GKMF EATAR GARRMAILGD TAWDFGSVGG VLNSLGKMVH QIFGSAYTAL FSGVSWVMKI GIGVLLTWIG LNSKNTSMSF SCIAI GIIT LYLGAVVQA

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Macromolecule #2: Membrane protein

MacromoleculeName: Membrane protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
SVALAPHVGM GLDTRTQTWM SAEGAWRQVE KVETWALRHP GFTILALFLA HYIGTSLTQK VVIFILLMLV TPSMT

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Macromolecule #3: Human antibody DENV-290 heavy chain

MacromoleculeName: Human antibody DENV-290 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVELVESGGD VVQPGKSLRL SCAASGFTFT NYAMHWLRQA PGKGLEWVAV ISSDVNDKYY ADSVKGRFTI SRDNSKNTLY LQMNSLTPE DTAVYYCARE QAVGTNPWAF DYWGQGTLVT VSS

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Macromolecule #4: Human antibody DENV-290 light chain

MacromoleculeName: Human antibody DENV-290 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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
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-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.

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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

Startup modelType of model: EMDB MAP
EMDB ID:

5933

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 154214
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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