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- PDB-3j82: Electron cryo-microscopy of DNGR-1 in complex with F-actin -

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Basic information

Entry
Database: PDB / ID: 3j82
TitleElectron cryo-microscopy of DNGR-1 in complex with F-actin
Components
  • Actin, cytoplasmic 1
  • C-type lectin domain family 9 member A
KeywordsMEMBRANE PROTEIN/ADP-BINDING PROTEIN / DNGR-1 / Actin / Recognition of damage-associated molecular patterns / MEMBRANE PROTEIN-ADP-BINDING PROTEIN complex
Function / homology
Function and homology information


positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton ...positive regulation of cytokine production => GO:0001819 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / Formation of annular gap junctions / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / Recycling pathway of L1 / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / brush border / kinesin binding / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / EPHB-mediated forward signaling / substantia nigra development / receptor-mediated endocytosis / axonogenesis / negative regulation of protein binding / cell motility / actin filament / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of transmembrane transporter activity / positive regulation of cell differentiation / FCGR3A-mediated phagocytosis / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / tau protein binding / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / nuclear matrix / VEGFA-VEGFR2 Pathway / UCH proteinases / 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 / nucleosome / cell-cell junction / Signaling by BRAF and RAF1 fusions / actin cytoskeleton / presynapse / lamellipodium / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones
Similarity search - Function
C-type lectin domain family 9 member A / Natural killer cell receptor-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 ...C-type lectin domain family 9 member A / Natural killer cell receptor-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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, cytoplasmic 1 / C-type lectin domain family 9 member A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsHanc, P. / Fujii, T. / Yamada, Y. / Huotari, J. / Schulz, O. / Ahrens, S. / Kjaer, S. / Way, M. / Namba, K. / Reis e Sousa, C.
CitationJournal: 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
DepositionSep 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references / Other
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn / em_image_scans / em_single_particle_entity / em_software / struct_conn
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_software.image_processing_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

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Assembly

Deposited unit
A: C-type lectin domain family 9 member A
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2848
Polymers139,9624
Non-polymers1,3224
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein C-type lectin domain family 9 member A / Dendritic cell natural killer lectin group receptor 1


Mass: 14968.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clec9a, Dngr-1 / Production host: Homo sapiens (human) / References: UniProt: Q8BRU4
#2: Protein Actin, cytoplasmic 1 / / Beta-actin / Actin / cytoplasmic 1 / N-terminally processed


Mass: 41664.484 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Human platelet actin / Source: (natural) Homo sapiens (human) / References: UniProt: P60709
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeParent-ID
1F-actin complexed with mouse DNGR-1 extracellular domainCOMPLEX0
2DNGR-11
3Actin1
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: R0.6/1.0, Quantifoil
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Dec 10, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Calibrated magnification: 109489 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 1.6 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Temperature: 55 K / Temperature (max): 60 K / Temperature (min): 50 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
EM imaging opticsEnergyfilter name: JEOL Omega filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: Each Particle
Helical symmertyAngular rotation/subunit: 166.6 ° / Axial rise/subunit: 27.6 Å / Axial symmetry: C1
3D reconstructionMethod: IHRSR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73608 / Details: (Single particle--Applied symmetry: C1) / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms9802 0 82 0 9884

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