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- EMDB-5935: Cryo-EM structure of Dengue virus serotype 3 in complex with huma... -

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Basic information

Entry
Database: EMDB / ID: EMD-5935
TitleCryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab
Map dataCryo-EM reconstruction of Dengue virus 3 in complex with human antibody 5J7 Fab
Sample
  • Sample: Dengue virus 3 complexed with human antibody 5J7 Fab
  • Virus: Dengue virus 3
  • Protein or peptide: antibody 5J7 Fab
Keywordsdengue virus / human antibody / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity ...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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / 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 NS3 helicase, C-terminal helical 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 / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Dengue virus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsFibriansah G / Tan JL / Smith SA / de Alwis R / Ng T-S / Kostyuchenko VA / Kukkaro P / de Silva AM / Crowe Jr JE / Lok S-M
CitationJournal: Nat Commun / Year: 2015
Title: A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins.
Authors: Guntur Fibriansah / Joanne L Tan / Scott A Smith / Ruklanthi de Alwis / Thiam-Seng Ng / Victor A Kostyuchenko / Ramesh S Jadi / Petra Kukkaro / Aravinda M de Silva / James E Crowe / Shee-Mei Lok /
Abstract: Dengue virus (DENV) infects ~400 million people annually. There is no licensed vaccine or therapeutic drug. Only a small fraction of the total DENV-specific antibodies in a naturally occurring dengue ...Dengue virus (DENV) infects ~400 million people annually. There is no licensed vaccine or therapeutic drug. Only a small fraction of the total DENV-specific antibodies in a naturally occurring dengue infection consists of highly neutralizing antibodies. Here we show that the DENV-specific human monoclonal antibody 5J7 is exceptionally potent, neutralizing 50% of virus at nanogram-range antibody concentration. The 9 Å resolution cryo-electron microscopy structure of the Fab 5J7-DENV complex shows that a single Fab molecule binds across three envelope proteins and engages three functionally important domains, each from a different envelope protein. These domains are critical for receptor binding and fusion to the endosomal membrane. The ability to bind to multiple domains allows the antibody to fully coat the virus surface with only 60 copies of Fab, that is, half the amount compared with other potent antibodies. Our study reveals a highly efficient and unusual mechanism of molecular recognition by an antibody.
History
DepositionMar 26, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseMar 4, 2015-
UpdateMar 4, 2015-
Current statusMar 4, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j6u
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j6u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5935.png

Downloads & links

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Map

FileDownload / File: emd_5935.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Dengue virus 3 in complex with human antibody 5J7 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 640 pix.
= 876.8 Å		1.37 Å/pix.
x 640 pix.
= 876.8 Å		1.37 Å/pix.
x 640 pix.
= 876.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 3
Minimum - Maximum-13.04963875 - 11.91217518
Average (Standard dev.)-0.14095771 (±0.98521209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 876.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z876.800876.800876.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-13.05011.912-0.141

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Supplemental data

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Sample components

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Entire : Dengue virus 3 complexed with human antibody 5J7 Fab

EntireName: Dengue virus 3 complexed with human antibody 5J7 Fab
Components
  • Sample: Dengue virus 3 complexed with human antibody 5J7 Fab
  • Virus: Dengue virus 3
  • Protein or peptide: antibody 5J7 Fab

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Supramolecule #1000: Dengue virus 3 complexed with human antibody 5J7 Fab

SupramoleculeName: Dengue virus 3 complexed with human antibody 5J7 Fab / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Dengue virus 3

SupramoleculeName: Dengue virus 3 / type: virus / ID: 1 / NCBI-ID: 11069 / Sci species name: Dengue virus 3 / Sci species strain: D3/SG/05K863DK1/2005 / 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: antibody 5J7 Fab

MacromoleculeName: antibody 5J7 Fab / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human

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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, 1 mM EDTA
GridDetails: ultra-thin carbon-coated lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / 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
DateMar 23, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 254 / Average electron dose: 18 e/Å2 / Bits/pixel: 16
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: 4.2 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 59000
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 reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: MPSA, EMAN, EMAN2 / Number images used: 970

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Atomic model buiding 1

Initial modelPDB ID:

3j6t


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F
SoftwareName: Chimera, Coot, NAMD/MDFF
DetailsInitially fitted in Chimera, model rebuilt in Coot, refined in NAMD/MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: real space correlation
Output model

PDB-3j6u:
Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab

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Atomic model buiding 2

Initial modelPDB ID:

3ma9

SoftwareName: Chimera, Coot, NAMD/MDFF
DetailsInitially fitted in Chimera, model rebuilt in Coot, refined in NAMD/MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: real space correlation
Output model

PDB-3j6u:
Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab

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Atomic model buiding 3

Initial modelPDB ID:

1dee

SoftwareName: Chimera, Coot, NAMD/MDFF
DetailsInitially fitted in Chimera, model rebuilt in Coot, refined in NAMD/MDFF
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: real space correlation
Output model

PDB-3j6u:
Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab

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