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- EMDB-1166: Cryo-EM reconstruction of dengue virus in complex with the carboh... -

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Basic information

Entry
Database: EMDB / ID: EMD-1166
TitleCryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN.
Map dataEM map of dengue virus in complex with CRD domain of DC-SIGN
Sample
  • Sample: Dengue virus complexed with CRD domain of DC-SIGN
  • Virus: Dengue-2
  • Protein or peptide: CRD domain of DC-SIGN
Function / homology
Function and homology information


B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation ...B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / RSV-host interactions / D-mannose binding / antigen processing and presentation / 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 / positive regulation of T cell proliferation / CD209 (DC-SIGN) signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral genome replication / ribonucleoside triphosphate phosphatase activity / endocytosis / peptide antigen binding / viral capsid / double-stranded RNA binding / host cell / channel activity / virus receptor activity / monoatomic ion transmembrane transport / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / intracellular signal transduction / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / symbiont-mediated activation of host autophagy / symbiont entry into host cell / external side of plasma membrane / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / : / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / cell surface / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...: / CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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 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 NS3 helicase, C-terminal helical domain / 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
CD209 antigen / CD209 antigen / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Dengue-2
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsPokidysheva E / Zhang Y / Battisti AJ / Bator-Kelly CM / Chipman PR / Xiao C / Gregorio GG / Hendrickson WA / Kuhn RJ / Rossmann MG
CitationJournal: Cell / Year: 2006
Title: Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN.
Authors: Elena Pokidysheva / Ying Zhang / Anthony J Battisti / Carol M Bator-Kelly / Paul R Chipman / Chuan Xiao / G Glenn Gregorio / Wayne A Hendrickson / Richard J Kuhn / Michael G Rossmann /
Abstract: Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), ...Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), abundant in immature dendritic cells, was previously reported as being an ancillary receptor interacting with the surface of DENV. The structure of DENV in complex with the carbohydrate recognition domain (CRD) of DC-SIGN was determined by cryo-electron microscopy at 25 A resolution. One CRD monomer was found to bind to two glycosylation sites at Asn67 of two neighboring glycoproteins in each icosahedral asymmetric unit, leaving the third Asn67 residue vacant. The vacancy at the third Asn67 site is a result of the nonequivalence of the glycoprotein environments, leaving space for the primary receptor binding to domain III of E. The use of carbohydrate moieties for receptor binding sites suggests a mechanism for avoiding immune surveillance.
History
DepositionSep 29, 2005-
Header (metadata) releaseOct 3, 2005-
Map releaseJul 3, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2b6b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1166.gif

Downloads & links

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Map

FileDownload / File: emd_1166.map.gz / Format: CCP4 / Size: 13.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of dengue virus in complex with CRD domain of DC-SIGN
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
4.34 Å/pix.
x 154 pix.
= 668.36 Å		4.34 Å/pix.
x 154 pix.
= 668.36 Å		4.34 Å/pix.
x 154 pix.
= 668.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.34 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.36 / Movie #1: 0
Minimum - Maximum-2.99261 - 4.39911
Average (Standard dev.)0.00208941 (±0.999885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-77-77-77
Dimensions154154154
Spacing154154154
CellA=B=C: 668.36 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.344.344.34
M x/y/z154154154
origin x/y/z0.0000.0000.000
length x/y/z668.360668.360668.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-77-77
NX/NY/NZ154154154
MAP C/R/S213
start NC/NR/NS-77-77-77
NC/NR/NS154154154
D min/max/mean-2.9934.3990.002

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Supplemental data

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Sample components

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Entire : Dengue virus complexed with CRD domain of DC-SIGN

EntireName: Dengue virus complexed with CRD domain of DC-SIGN
Components
  • Sample: Dengue virus complexed with CRD domain of DC-SIGN
  • Virus: Dengue-2
  • Protein or peptide: CRD domain of DC-SIGN

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Supramolecule #1000: Dengue virus complexed with CRD domain of DC-SIGN

SupramoleculeName: Dengue virus complexed with CRD domain of DC-SIGN / type: sample / ID: 1000 / Details: Calcium should be present in the sample. / Oligomeric state: one monomer of CRD binds virus ico / Number unique components: 2
Molecular weightTheoretical: 12 MDa

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Supramolecule #1: Dengue-2

SupramoleculeName: Dengue-2 / type: virus / ID: 1 / Sci species name: Dengue-2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 11 MDa / Theoretical: 11 MDa
Virus shellShell ID: 1 / Name: outer shell, T is not applicable / Diameter: 500 Å / T number (triangulation number): 3

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Macromolecule #1: CRD domain of DC-SIGN

MacromoleculeName: CRD domain of DC-SIGN / type: protein_or_peptide / ID: 1
Details: expressed insoluble in the inclusion bodies. Refolded.
Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: dendritic cells / Cell: bacteria BL21-DE3 / Location in cell: cell membrane, extracellular matrix
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pet 28

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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

Concentration2 mg/mL
BufferpH: 7.5
Details: 50mM Tris 50mM NaCl 0.5 mM EDTA, 5 mM CaCl2, pH 7.5
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Guillotine-style plunge freezeing device
Method: Small aliquots of sample were applied to 400 mesh copper grids coated with holey carbon film and rapidly frozen by plunging into an ethane slush

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 103 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 98,000 times magnification
DateNov 15, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 45 / Average electron dose: 11.8 e/Å2 / Od range: 1.1 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder: Cryo / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailsthe particles were selected manualy
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider / Number images used: 830
Final angle assignmentDetails: SPIDER theta 36.4 degrees, phi 72 degrees

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