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- EMDB-2968: Cryo-EM structure of Dengue virus serotype 2 strain New Guinea-C ... -

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Entry
Database: EMDB / ID: EMD-2968
TitleCryo-EM structure of Dengue virus serotype 2 strain New Guinea-C complexed with human antibody 2D22 Fab at 37 degree C. The Fab molecules were added to the virus before 37 degree C incubation.
Map dataReconstruction of Dengue Virus serotype 2 strain New Guinea-C in complex with human antibody 2D22 Fab at 37 degree C. The Fab molecules were added to the virus before 37 degree incubation.
Sample
  • Sample: Dengue virus serotype 2 strain New Guinea-C complexed with Fab fragments of human antibody 2D22 at 37 degree C.
  • Virus: Dengue Virus serotype 2
  • Protein or peptide: antigen-binding fragment of human antibody 2D22
Keywordsdengue virus / dengue serotype 2 / human antibody / cryo-EM / neutralization
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / viral capsid / monoatomic ion transmembrane transport ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / viral capsid / monoatomic ion transmembrane transport / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / 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 central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Dengue Virus serotype 2
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsFibriansah G / Ibarra KD / Ng TS / Smith SA / Tan JL / Lim XN / Ooi JSG / Kostyuchenko VA / Wang J / de Silva AM ...Fibriansah G / Ibarra KD / Ng TS / Smith SA / Tan JL / Lim XN / Ooi JSG / Kostyuchenko VA / Wang J / de Silva AM / Harris E / Crowe JE / Lok SM
CitationJournal: Science / Year: 2015
Title: DENGUE VIRUS. Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers.
Authors: Guntur Fibriansah / Kristie D Ibarra / Thiam-Seng Ng / Scott A Smith / Joanne L Tan / Xin-Ni Lim / Justin S G Ooi / Victor A Kostyuchenko / Jiaqi Wang / Aravinda M de Silva / Eva Harris / ...Authors: Guntur Fibriansah / Kristie D Ibarra / Thiam-Seng Ng / Scott A Smith / Joanne L Tan / Xin-Ni Lim / Justin S G Ooi / Victor A Kostyuchenko / Jiaqi Wang / Aravinda M de Silva / Eva Harris / James E Crowe / Shee-Mei Lok /
Abstract: There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. ...There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. We demonstrated that DENV serotype 2 (DENV2)-specific human monoclonal antibody (HMAb) 2D22 is therapeutic in a mouse model of antibody-enhanced severe dengue disease. We determined the cryo-electron microscopy (cryo-EM) structures of HMAb 2D22 complexed with two different DENV2 strains. HMAb 2D22 binds across viral envelope (E) proteins in the dimeric structure, which probably blocks the E protein reorganization required for virus fusion. HMAb 2D22 "locks" two-thirds of or all dimers on the virus surface, depending on the strain, but neutralizes these DENV2 strains with equal potency. The epitope defined by HMAb 2D22 is a potential target for vaccines and therapeutics.
History
DepositionMar 30, 2015-
Header (metadata) releaseApr 15, 2015-
Map releaseJul 15, 2015-
UpdateJul 22, 2015-
Current statusJul 22, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
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  • Surface view colored by radius
  • Surface level: 1.5
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  • Surface view with fitted model
  • Atomic models: PDB-4uih
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4uih
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_2968.png

Downloads & links

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Map

FileDownload / File: emd_2968.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Dengue Virus serotype 2 strain New Guinea-C in complex with human antibody 2D22 Fab at 37 degree C. The Fab molecules were added to the virus before 37 degree incubation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 512 pix.
= 865.28 Å		1.69 Å/pix.
x 512 pix.
= 865.28 Å		1.69 Å/pix.
x 512 pix.
= 865.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-8.583108899999999 - 10.9272337
Average (Standard dev.)-0.10779313 (±1.00290585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 865.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z865.280865.280865.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-8.58310.927-0.108

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Supplemental data

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Sample components

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Entire : Dengue virus serotype 2 strain New Guinea-C complexed with Fab fr...

EntireName: Dengue virus serotype 2 strain New Guinea-C complexed with Fab fragments of human antibody 2D22 at 37 degree C.
Components
  • Sample: Dengue virus serotype 2 strain New Guinea-C complexed with Fab fragments of human antibody 2D22 at 37 degree C.
  • Virus: Dengue Virus serotype 2
  • Protein or peptide: antigen-binding fragment of human antibody 2D22

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Supramolecule #1000: Dengue virus serotype 2 strain New Guinea-C complexed with Fab fr...

SupramoleculeName: Dengue virus serotype 2 strain New Guinea-C complexed with Fab fragments of human antibody 2D22 at 37 degree C.
type: sample / ID: 1000
Details: The Fab molecules were mixed with the virus before 37 degree C incubation
Number unique components: 2

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Supramolecule #1: Dengue Virus serotype 2

SupramoleculeName: Dengue Virus serotype 2 / type: virus / ID: 1 / Sci species name: Dengue Virus serotype 2 / Sci species strain: New Guinea-C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Aedes albopictus (Asian tiger mosquito) / Recombinant cell: C6/36

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Macromolecule #1: antigen-binding fragment of human antibody 2D22

MacromoleculeName: antigen-binding fragment of human antibody 2D22 / type: protein_or_peptide / ID: 1 / Details: 120 copies of Fab molecules bind to virus surface / Number of copies: 120 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: memory B-cells

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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: 10 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA
GridDetails: ultra-thin carbon-coated lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: blotted with filter paper for 2 seconds prior to snap freezing

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 100 K
DateJun 13, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 168 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0036 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were manually selected
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, MPSA / Number images used: 4288

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Atomic model buiding 1

Initial modelPDB ID:

4uif


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: C / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: I / Chain - #4 - Chain ID: J / Chain - #5 - Chain ID: K / Chain - #6 - Chain ID: L
SoftwareName: Program O
DetailsThe protein molecules were fitted by manual docking using program O
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4uih:
Cryo-EM structure of Dengue virus serotype 2 strain New Guinea-C complexed with human antibody 2D22 Fab at 37 degree C. The Fab molecules were added to the virus before 37 degree C incubation.

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