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- EMDB-70931: CryoEM structure of stabilized dengue 3 virus envelope glycoprote... -

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Basic information

Entry
Database: EMDB / ID: EMD-70931
TitleCryoEM structure of stabilized dengue 3 virus envelope glycoprotein in complex with Fab of F25.S01
Map dataSharpened map of F25.S02 bound to DenV3 sE sc30 dimer
Sample
  • Complex: Complex of F25.S02 Fab bound to DenV3 sE sc30
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: F25.S02 Heavy chain
    • Protein or peptide: F25.S02 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsOrthoflavivirus / Dengue / IMMUNE SYSTEM
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 speciesHomo sapiens (human) / dengue virus type 3
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsHurlburt NK / Pancera M
Funding support1 items
OrganizationGrant numberCountry
Other privateFred Hutchinson Cancer Center
CitationJournal: To Be Published
Title: Structural basis for antibody cross-neutralization of dengue and Zika viruses
Authors: Hurlburt NK / Pancera M
History
DepositionJun 2, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70931.png

Downloads & links

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Map

FileDownload / File: emd_70931.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of F25.S02 bound to DenV3 sE sc30 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 359.04 Å		1.12 Å/pix.
x 320 pix.
= 359.04 Å		1.12 Å/pix.
x 320 pix.
= 359.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.2393348 - 4.310036
Average (Standard dev.)0.0018739523 (±0.08489051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 359.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A of F25.S02 bound to DenV3 sE sc30 dimer

Fileemd_70931_half_map_1.map
AnnotationHalf-map A of F25.S02 bound to DenV3 sE sc30 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of F25.S02 bound to DenV3 sE sc30 dimer

Fileemd_70931_half_map_2.map
AnnotationHalf-map B of F25.S02 bound to DenV3 sE sc30 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of F25.S02 Fab bound to DenV3 sE sc30

EntireName: Complex of F25.S02 Fab bound to DenV3 sE sc30
Components
  • Complex: Complex of F25.S02 Fab bound to DenV3 sE sc30
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: F25.S02 Heavy chain
    • Protein or peptide: F25.S02 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of F25.S02 Fab bound to DenV3 sE sc30

SupramoleculeName: Complex of F25.S02 Fab bound to DenV3 sE sc30 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 3
Molecular weightTheoretical: 45.00132 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRCVGVGNRD FVEGLSGATW VDVVLEHGKC VTVMMKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCDLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST ...String:
MRCVGVGNRD FVEGLSGATW VDVVLEHGKC VTVMMKNKPT LDIELQKTEA TQLATLRKLC IEGKITNITT DSRCPTQGEA ILPEEQDQN YVCKHTYVDR GWGNGCDLFG KGSLVTCAKF QCLESIEGKV VQHENLKYTV IITVHTGDQH QVGNETQGVT A EITPQAST VEAILPEYGT LGLECSPRTG LDFNEMILLT MKNKAWMVHR QWFFDLPLPW TSGATTETPT WNRKELLVTF KN AHAKKQE VVVLGSQEGC MHTALTGATE IQNSGGTSIW PGHLKCRLKM DKLELKGMSY AMCLNTFVLK KEVSETQHGT ILI KVEYKG EDAPCKIPFS TEDGQGKAHN GRLITANPVV TKKEEPVNIE AEPPFGESNI VIGIGDKALK INWYKKGSSG GSHH HHHHH H

UniProtKB: Genome polyprotein

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Macromolecule #2: F25.S02 Heavy chain

MacromoleculeName: F25.S02 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.57567 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (PCA)VQLVQSGAE VKKPGSSAKV SCKASGGTFS SYAISWVRQA PGQGLEWMGS IMPIFGTVNY AQKFQGRVTI TADEST STA YMELSRLRSE DTAVYFCARG WGGNYRSADL WIYFDLWGQG TLVTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVK DY FPEPVTVSWN ...String:
(PCA)VQLVQSGAE VKKPGSSAKV SCKASGGTFS SYAISWVRQA PGQGLEWMGS IMPIFGTVNY AQKFQGRVTI TADEST STA YMELSRLRSE DTAVYFCARG WGGNYRSADL WIYFDLWGQG TLVTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVK DY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CDKTHHHH H H

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Macromolecule #3: F25.S02 Light chain

MacromoleculeName: F25.S02 Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.023486 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPRSV SGSPGQSVTI SCTGTSSDVG GYKYVSWYQQ HPGKAPKLMI YDVTKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYAGSYTH VVFGGGTKLT VLGQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSALTQPRSV SGSPGQSVTI SCTGTSSDVG GYKYVSWYQQ HPGKAPKLMI YDVTKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYAGSYTH VVFGGGTKLT VLGQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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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: 2 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7a3p

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111111
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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