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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 norepinephrine uptake / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Formation of the polybromo-BAF (pBAF) complex ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Formation of the polybromo-BAF (pBAF) complex / Gap junction degradation / GBP-mediated host defense / protein localization to adherens junction / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / dense body / Folding of actin by CCT/TriC / Tat protein binding / postsynaptic actin cytoskeleton / Regulation of CDH1 Function / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / regulation of double-strand break repair / microtubule nucleation / adherens junction assembly / RHOF GTPase cycle / Sensory processing of sound by outer hair cells of the cochlea / tight junction / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / apical junction complex / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / Recycling pathway of L1 / cortical cytoskeleton / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / establishment or maintenance of cell polarity / nitric-oxide synthase binding / brush border / EPH-ephrin mediated repulsion of cells / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / kinesin binding / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / axonogenesis / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / receptor-mediated endocytosis / calyx of Held / cell motility / nitric-oxide synthase regulator activity / positive regulation of cytokine production / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / B-WICH complex positively regulates rRNA expression / tau protein binding / Schaffer collateral - CA1 synapse / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic ribonucleoprotein granule / structural constituent of cytoskeleton / kinetochore / nuclear matrix / Signaling by RAF1 mutants / cell-cell junction / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin cytoskeleton / Signaling by BRAF and RAF1 fusions / UCH proteinases / lamellipodium / presynapse / 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
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water00
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


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

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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 FIELD / 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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