+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6102 | |||||||||
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Title | Electron cryo-microscopy of DNGR-1 in complex with F-actin | |||||||||
Map data | Reconstruction of DNGR1 in complex with F-actin | |||||||||
Sample |
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Keywords | DNGR-1 / Actin / Damage-associated molecular patterns | |||||||||
Function / homology | Function and homology information positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction ...positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / receptor-mediated endocytosis / axonogenesis / negative regulation of protein binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / cell motility / RHO GTPases Activate Formins / positive regulation of cell differentiation / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by high-kinase activity BRAF mutants / DNA Damage Recognition in GG-NER / MAP2K and MAPK activation / B-WICH complex positively regulates rRNA expression / tau protein binding / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / nuclear matrix / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / nucleosome / Signaling by BRAF and RAF1 fusions / cell-cell junction / Clathrin-mediated endocytosis / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / lamellipodium / presynapse Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Hanc P / Fujii T / Yamada Y / Huotari J / Schulz O / Ahrens S / Kjaer S / Way M / Namba K / Reis e Sousa C | |||||||||
Citation | Journal: Immunity / Year: 2015 Title: Structure of the Complex of F-Actin and DNGR-1, a C-Type Lectin Receptor Involved in Dendritic Cell Cross-Presentation of Dead Cell-Associated Antigens. Authors: Pavel Hanč / Takashi Fujii / Salvador Iborra / Yurika Yamada / Jatta Huotari / Oliver Schulz / Susan Ahrens / Svend Kjær / Michael Way / David Sancho / Keiichi Namba / Caetano Reis e Sousa / Abstract: DNGR-1 is a C-type lectin receptor that binds F-actin exposed by dying cells and facilitates cross-presentation of dead cell-associated antigens by dendritic cells. Here we present the structure of ...DNGR-1 is a C-type lectin receptor that binds F-actin exposed by dying cells and facilitates cross-presentation of dead cell-associated antigens by dendritic cells. Here we present the structure of DNGR-1 bound to F-actin at 7.7 Å resolution. Unusually for F-actin binding proteins, the DNGR-1 ligand binding domain contacts three actin subunits helically arranged in the actin filament, bridging over two protofilaments, as well as two neighboring actin subunits along one protofilament. Mutation of residues predicted to mediate ligand binding led to loss of DNGR-1-dependent cross-presentation of dead cell-associated antigens, formally demonstrating that the latter depends on F-actin recognition. Notably, DNGR-1 has relatively modest affinity for F-actin but multivalent interactions allow a marked increase in binding strength. Our findings shed light on modes of actin binding by cellular proteins and reveal how extracellular detection of cytoskeletal components by dedicated receptors allows immune monitoring of loss of cellular integrity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6102.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-6102-v30.xml emd-6102.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | 400_6102.gif 80_6102.gif | 40.5 KB 4.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6102 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6102 | HTTPS FTP |
-Validation report
Summary document | emd_6102_validation.pdf.gz | 329 KB | Display | EMDB validaton report |
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Full document | emd_6102_full_validation.pdf.gz | 328.6 KB | Display | |
Data in XML | emd_6102_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6102 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6102 | HTTPS FTP |
-Related structure data
Related structure data | 3j82MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6102.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of DNGR1 in complex with F-actin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : F-actin complexed with mouse DNGR-1 extracellular domain
Entire | Name: F-actin complexed with mouse DNGR-1 extracellular domain |
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Components |
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-Supramolecule #1000: F-actin complexed with mouse DNGR-1 extracellular domain
Supramolecule | Name: F-actin complexed with mouse DNGR-1 extracellular domain type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: DNGR-1
Macromolecule | Name: DNGR-1 / type: protein_or_peptide / ID: 1 / Name.synonym: CLEC9A / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: Mouse |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 25mM Hepes buffer (pH 7.5), 100mM KCl, 1mM MgCl2, 1mM ATP |
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Grid | Details: R0.6/1.0, Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 50 K / Max: 60 K / Average: 55 K |
Specialist optics | Energy filter - Name: JEOL Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Dec 10, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 774 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 109489 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
CTF correction | Details: Each Particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: OTHER / Software - Name: Spider, EMAN / Number images used: 73608 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D |
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Software | Name: Spider, EMAN |
Details | Single particle--Applied symmetry: C1 |
Refinement | Space: REAL |
Output model | PDB-3j82: |