[English] 日本語
Yorodumi
- EMDB-1166: Cryo-EM reconstruction of dengue virus in complex with the carboh... -

+
Open data


ID or keywords:

Loading...

-
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 / pattern recognition receptor activity ...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 / pattern recognition receptor activity / RSV-host interactions / antigen processing and presentation / D-mannose binding / regulation of T cell proliferation / 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 / peptide antigen binding / endocytosis / viral capsid / double-stranded RNA binding / host cell / virus receptor activity / channel activity / carbohydrate binding / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / protein dimerization activity / RNA helicase activity / intracellular signal transduction / host cell endoplasmic reticulum membrane / 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 / innate immune response / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / : / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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
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

-
Structure visualization

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

1166.gif

Downloads & links

-
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more