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- PDB-2b6b: Cryo EM structure of Dengue complexed with CRD of DC-SIGN -

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Basic information

Entry
Database: PDB / ID: 2b6b
TitleCryo EM structure of Dengue complexed with CRD of DC-SIGN
Components
  • CD209 antigen
  • envelope glycoprotein
KeywordsVirus/Receptor / Cryo EM dengue CRD DC-SIGN / Icosahedral virus / Virus-Receptor COMPLEX
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 / 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 / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / CD209 (DC-SIGN) signaling / ribonucleoside triphosphate phosphatase activity / viral genome replication / peptide antigen binding / endocytosis / viral capsid / host cell / double-stranded RNA binding / channel activity / virus receptor activity / carbohydrate binding / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / adaptive immune response / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / intracellular signal transduction / host cell perinuclear region of cytoplasm / immune response / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / innate immune response / external side of plasma membrane / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / cell surface / proteolysis / extracellular region / ATP binding / metal ion binding / membrane / 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 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 virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 25 Å
AuthorsPokidysheva, E. / Zhang, Y. / Battisti, A.J. / Bator-Kelly, C.M. / Chipman, P.R. / Gregorio, G. / Hendrickson, W.A. / Kuhn, R.J. / Rossmann, M.G.
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 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details
Remark 999SEQUENCE The proteins in this entry contain CA only.

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1166
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  • Simplified surface model + fitted atomic model
  • EMDB-1167
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Structure viewerMolecule:
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Assembly

Deposited unit
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
D: CD209 antigen


Theoretical massNumber of molelcules
Total (without water)151,3784
Polymers151,3784
Non-polymers00
Water00
1
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
D: CD209 antigen
x 60


Theoretical massNumber of molelcules
Total (without water)9,082,692240
Polymers9,082,692240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
D: CD209 antigen
x 5


  • icosahedral pentamer
  • 757 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)756,89120
Polymers756,89120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
D: CD209 antigen
x 6


  • icosahedral 23 hexamer
  • 908 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)908,26924
Polymers908,26924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein envelope glycoprotein / Coordinate model: Cα atoms only


Mass: 43819.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dengue virus / Genus: Flavivirus / References: GenBank: 323503, UniProt: Q9WDA7*PLUS
#2: Protein CD209 antigen / Dendritic cell-specific ICAM-3-grabbing nonintegrin 1 / DC-SIGN1 / DC-SIGN / Coordinate model: Cα atoms only


Mass: 19920.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QQ4, UniProt: Q9NNX6*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DENGUE VIRUS COMPLEXED WITH CRD OF DC-SIGN / Type: VIRUS
Details of virusHost category: INSECT / Type: VIRION
Natural hostStrain: C6/36
Buffer solutionpH: 7.5
Details: 50mM Tris 50mM NaCl 0.5 mM EDTA, 5 mM CaCl2, pH 7.5
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Nov 15, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 87 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 27 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2SPIDER3D reconstruction
CTF correctionDetails: EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER*(1-|CTF|)]
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: MODEL-BASED / Resolution: 25 Å / Num. of particles: 830 / Nominal pixel size: 2.95 Å / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--PLEASE SEE CITATION
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11THD

1thd

11THD1PDBexperimental model
21K9I

1k9i

11K9I2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 0 0 1295

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