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- EMDB-38886: Cryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-38886
TitleCryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 in complex with human antibody C10 Fab at 37 deg C
Map data
Sample
  • Virus: dengue virus type 2
    • Complex: Dengue serotype 2 strain D2Y98P-PP1
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane polyprotein
    • Complex: Human antibody C10 Fab (heavy and light chains)
      • Protein or peptide: Human antibody C10 Fab (heavy chain)
      • Protein or peptide: Human antibody C10 Fab (light chain)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsdengue virus / human antibody / dengue-antibody structure / virus / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral capsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane ...viral capsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / extracellular region / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily ...Flavivirus capsid protein C superfamily / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / 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 speciesdengue virus type 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFibriansah G / Ng TS / Lim XN / Tan AWK / Shi J / Lok SM
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Other governmentMOH-OFIRG18may-0007 Singapore
CitationJournal: To Be Published
Title: Role of N-glycosylation at asparagine 153 of dengue envelope protein in immune response
Authors: Fibriansah G / Ng TS / Lim XN / Tan AWK / Shi J / Crowe JE / Lok SM
History
DepositionJan 29, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38886.png

Downloads & links

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Map

FileDownload / File: emd_38886.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 512 pix.
= 679.936 Å		1.33 Å/pix.
x 512 pix.
= 679.936 Å		1.33 Å/pix.
x 512 pix.
= 679.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-8.991622 - 16.875340000000001
Average (Standard dev.)-0.000000002780007 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 679.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38886_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_38886_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_38886_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 type 2

EntireName: dengue virus type 2
Components
  • Virus: dengue virus type 2
    • Complex: Dengue serotype 2 strain D2Y98P-PP1
      • Protein or peptide: Envelope protein
      • Protein or peptide: Membrane polyprotein
    • Complex: Human antibody C10 Fab (heavy and light chains)
      • Protein or peptide: Human antibody C10 Fab (heavy chain)
      • Protein or peptide: Human antibody C10 Fab (light chain)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: dengue virus type 2

SupramoleculeName: dengue virus type 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Supramolecule #2: Dengue serotype 2 strain D2Y98P-PP1

SupramoleculeName: Dengue serotype 2 strain D2Y98P-PP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: dengue virus type 2

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Supramolecule #3: Human antibody C10 Fab (heavy and light chains)

SupramoleculeName: Human antibody C10 Fab (heavy and light chains) / 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 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 2 / Strain: D2Y98P
Molecular weightTheoretical: 54.286605 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString: MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KHPATLRKYC IEAKLTNTTT ASRCPTQGEP SLNEEQDKR FVCKHSMVDR GWGNGCGLFG KGGIVTCAMF TCKKNMEGKI VQPENLEYTI VITPHSGEEN AVGNDTGKHG K EIKVTPQS ...String:
MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KHPATLRKYC IEAKLTNTTT ASRCPTQGEP SLNEEQDKR FVCKHSMVDR GWGNGCGLFG KGGIVTCAMF TCKKNMEGKI VQPENLEYTI VITPHSGEEN AVGNDTGKHG K EIKVTPQS SITEAELTGY GTVTMECSPR TGLDFNEMVL LQMENKAWLV HRQWFLDLPL PWLPGADTQG SNWIQKETLV TF KNPHAKK QDVVVLGSQE GAMHTALTGA TEIQMSSGNL LFTGHLKCRL RMDKLQLKGM SYSMCTGKFK VVKEIAETQH GTI VIRVQY EGDGSPCKIP FEIMDLEKRH VLGRLITVNP IVTEKDSPVN IEAEPPFGDS YIIIGVEPGQ LKLSWFKKGS SIGQ MFETT MRGAKRMAIL GDTAWDFGSL GGVFTSIGKA LHQVFGAIYG AAFSGVSWTM KILIGVVITW IGMNSRSTSL SVSLV LVGV VTLYLGVMVQ A

UniProtKB: Genome polyprotein

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Macromolecule #2: Membrane polyprotein

MacromoleculeName: Membrane polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 2 / Strain: D2Y98P
Molecular weightTheoretical: 8.384814 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
SVALVPHVGM GLETRTETWM SSEGAWKHAQ RIETWVLRHP GFTIMAAILA YTIGTTYFQR VLIFILLTAV APSMT

UniProtKB: Genome polyprotein

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Macromolecule #3: Human antibody C10 Fab (heavy chain)

MacromoleculeName: Human antibody C10 Fab (heavy chain) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.487058 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGAE VKKPGASVKV SCKASGYTFT SYAMHWVRQA PGQRLEWMGW INAGNGNTKY SQKFQDRVTI TRDTSASTAY MELSSLRSE DTAIYYCARD KVDDYGDYWF PTLWYFDYWG QGTLVTVS

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Macromolecule #4: Human antibody C10 Fab (light chain)

MacromoleculeName: Human antibody C10 Fab (light chain) / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.51357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SQSALTQPAS VSGSPGQSIT ISCTGTSSDV GGFNYVSWFQ QHPGKAPKLM LYDVTSRPSG VSSRFSGSKS GNTASLTISG LQAEDEADY YCSSHTSRGT WVFGGGTKLT VL

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 human antibody C10 Fab at a molar ratio of 1.5 Fab for every E-protein and the mixture was incubated at 4 deg C for 30 min, and then at 37 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: 24.43 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 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:

2485

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 64522
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

4uif

source_name: PDB, initial_model_type: experimental model

7v3h

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

PDB-8y3l:
Cryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 in complex with human antibody C10 Fab at 37 deg C

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