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- EMDB-30886: Cryo-EM map of Dengue virus serotype 2 strain PVP94/07 in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-30886
TitleCryo-EM map of Dengue virus serotype 2 strain PVP94/07 in complex with human antibody 1C19 Fab at 40 deg C
Map dataCryoEM map of DENV2 strain PVP94/07 in complex with Fab 1C19 at 40 deg C
Sample
  • Complex: Dengue virus serotype 2 strain PVP94/07 in complex with human antibody 1C19 Fab
    • Complex: Dengue virus 2
      • Protein or peptide: Dengue virus serotype 2 strain PVP94/07 envelope protein
      • Protein or peptide: Dengue virus serotype 2 strain PVP94/07 membrane protein
    • Complex: human antibody 1C19 Fab
      • Protein or peptide: Anti-dengue virus human monoclonal antibody 1C19 Fab heavy chain
      • Protein or peptide: Anti-dengue virus human monoclonal antibody 1C19 Fab light chain
Biological speciesDengue virus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.0 Å
AuthorsFibriansah G / Ng TS / Kostyuchenko VA / Shi J / Lok SM
Funding support Singapore, United States, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
National Research Foundation (NRF, Singapore)NRF2017NRF-CRP001-027 Singapore
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI 057157 United States
CitationJournal: PLoS Pathog / Year: 2021
Title: Antibody affinity versus dengue morphology influences neutralization.
Authors: Guntur Fibriansah / Elisa X Y Lim / Jan K Marzinek / Thiam-Seng Ng / Joanne L Tan / Roland G Huber / Xin-Ni Lim / Valerie S Y Chew / Victor A Kostyuchenko / Jian Shi / Ganesh S Anand / Peter ...Authors: Guntur Fibriansah / Elisa X Y Lim / Jan K Marzinek / Thiam-Seng Ng / Joanne L Tan / Roland G Huber / Xin-Ni Lim / Valerie S Y Chew / Victor A Kostyuchenko / Jian Shi / Ganesh S Anand / Peter J Bond / James E Crowe / Shee-Mei Lok /
Abstract: Different strains within a dengue serotype (DENV1-4) can have smooth, or "bumpy" surface morphologies with different antigenic characteristics at average body temperature (37°C). We determined the ...Different strains within a dengue serotype (DENV1-4) can have smooth, or "bumpy" surface morphologies with different antigenic characteristics at average body temperature (37°C). We determined the neutralizing properties of a serotype cross-reactive human monoclonal antibody (HMAb) 1C19 for strains with differing morphologies within the DENV1 and DENV2 serotypes. We mapped the 1C19 epitope to E protein domain II by hydrogen deuterium exchange mass spectrometry, cryoEM and molecular dynamics simulations, revealing that this epitope is likely partially hidden on the virus surface. We showed the antibody has high affinity for binding to recombinant DENV1 E proteins compared to those of DENV2, consistent with its strong neutralizing activities for all DENV1 strains tested regardless of their morphologies. This finding suggests that the antibody could out-compete E-to-E interaction for binding to its epitope. In contrast, for DENV2, HMAb 1C19 can only neutralize when the epitope becomes exposed on the bumpy-surfaced particle. Although HMAb 1C19 is not a suitable therapeutic candidate, this study with HMAb 1C19 shows the importance of choosing a high-affinity antibody that could neutralize diverse dengue virus morphologies for therapeutic purposes.
History
DepositionJan 18, 2021-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30886.png

Downloads & links

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Map

FileDownload / File: emd_30886.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of DENV2 strain PVP94/07 in complex with Fab 1C19 at 40 deg C
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: 1.7 / Movie #1: 1.7
Minimum - Maximum-5.8288817 - 7.0135083
Average (Standard dev.)4.3742387e-09 (±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 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z875.520875.520875.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-5.8297.0140.000

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Supplemental data

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Sample components

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Entire : Dengue virus serotype 2 strain PVP94/07 in complex with human ant...

EntireName: Dengue virus serotype 2 strain PVP94/07 in complex with human antibody 1C19 Fab
Components
  • Complex: Dengue virus serotype 2 strain PVP94/07 in complex with human antibody 1C19 Fab
    • Complex: Dengue virus 2
      • Protein or peptide: Dengue virus serotype 2 strain PVP94/07 envelope protein
      • Protein or peptide: Dengue virus serotype 2 strain PVP94/07 membrane protein
    • Complex: human antibody 1C19 Fab
      • Protein or peptide: Anti-dengue virus human monoclonal antibody 1C19 Fab heavy chain
      • Protein or peptide: Anti-dengue virus human monoclonal antibody 1C19 Fab light chain

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Supramolecule #1: Dengue virus serotype 2 strain PVP94/07 in complex with human ant...

SupramoleculeName: Dengue virus serotype 2 strain PVP94/07 in complex with human antibody 1C19 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Dengue virus serotype 2 strain PVP94/07 was grown in Aedes albopictus C6/36 cells.
Source (natural)Organism: Dengue virus 2 / Strain: PVP94/07

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Supramolecule #2: Dengue virus 2

SupramoleculeName: Dengue virus 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 / Details: Dengue virus serotype 2 strain PVP94/07

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Supramolecule #3: human antibody 1C19 Fab

SupramoleculeName: human antibody 1C19 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 / Details: human antibody

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Macromolecule #1: Dengue virus serotype 2 strain PVP94/07 envelope protein

MacromoleculeName: Dengue virus serotype 2 strain PVP94/07 envelope protein
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus 2 / Strain: PVP94/07
SequenceString: MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KHPATLRKYC VEAKLTNTTT ASRCPTQGEP SLNEEQDKRF VCKHSMVDRG WGNGCGLFGK GGIVTCAMFT CKKNMEGKVV QPENLEYTIV ITPHSGEENA VGNDTGKHGK EIKVTPQSSI ...String:
MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KHPATLRKYC VEAKLTNTTT ASRCPTQGEP SLNEEQDKRF VCKHSMVDRG WGNGCGLFGK GGIVTCAMFT CKKNMEGKVV QPENLEYTIV ITPHSGEENA VGNDTGKHGK EIKVTPQSSI TEAELTGYGT VTMECSPRTG LDFNEMVLLQ MENKAWLVHR QWFLDLPLPW LPGADTQGSN WIQKETLVTF KNPHAKKQDV VVLGSQEGAM HTALTGATEI QMSSGNLLFT GHLKCRLRMD KLQLKGMSYS MCTGKFKVVK EIAETQHGTI VIRVQYEGDG SPCKIPFEIM DLEKRHVLGR LITVNPIVTE KDSPVNIEAE PPFGDSYIII GVEPGQLKLS WFKKGSSIGQ MFETTMRGAK RMAILGDTAW DFGSLGGVFT SIGKALHQVF GAIYGAAFSG VSWTMKILIG VVITWIGMNS RSTSLSVSLV LVGVVTLYLG VMVQA

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Macromolecule #2: Dengue virus serotype 2 strain PVP94/07 membrane protein

MacromoleculeName: Dengue virus serotype 2 strain PVP94/07 membrane protein
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Dengue virus 2 / Strain: PVP94/07
SequenceString:
SVALVPHVGM GLETRTETWM SSEGAWKHAQ RIETWILRHP GFTIMAAILA YTIGTTYFQR VLIFILLTAV TP

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Macromolecule #3: Anti-dengue virus human monoclonal antibody 1C19 Fab heavy chain

MacromoleculeName: Anti-dengue virus human monoclonal antibody 1C19 Fab heavy chain
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFIFS NYGMHWVRQA PGKGLEWVAV ISYDGSDKRY ADSVRGRFT ISRDNSKNTL FLQVTSLRAE DTAVYYCAKE LSGYDPGFEY WGQGTPVTVS S

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Macromolecule #4: Anti-dengue virus human monoclonal antibody 1C19 Fab light chain

MacromoleculeName: Anti-dengue virus human monoclonal antibody 1C19 Fab light chain
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQSIN TWLAWYQQKP GKAPKLLIYK ASSLESGVPS RFSGSGSGT EFTLTISSLQ PDDFATYYCQ QYESYATFGQ GTKVDIK

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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 incubated with Fab 1C19 at 40 deg C for 30 min with a molar ratio of one Fab for every E-protein and followed by incubation at 4 deg C for 2 h.

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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: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 37568
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER
Details: CryoEM map of Dengue virus serotype 2 strain PVP94/07 at 29 deg C
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA / Number images used: 15360
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: COMMON LINE / Software - Name: MPSA

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