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- EMDB-6102: Electron cryo-microscopy of DNGR-1 in complex with F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-6102
TitleElectron cryo-microscopy of DNGR-1 in complex with F-actin
Map dataReconstruction of DNGR1 in complex with F-actin
Sample
  • Sample: F-actin complexed with mouse DNGR-1 extracellular domain
  • Protein or peptide: DNGR-1
KeywordsDNGR-1 / Actin / Damage-associated molecular patterns
Function / homology
Function and homology information


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 / protein localization to adherens junction / nBAF complex / brahma complex ...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 / protein localization to adherens junction / nBAF complex / brahma complex / Tat protein binding / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Formation of annular gap junctions / regulation of G0 to G1 transition / Gap junction degradation / dense body / 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 / Adherens junctions interactions / tight junction / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / regulation of norepinephrine uptake / regulation of synaptic vesicle endocytosis / positive regulation of double-strand break repair / apical junction complex / positive regulation of T cell differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / cortical cytoskeleton / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / kinesin binding / negative regulation of cell differentiation / calyx of Held / EPH-ephrin mediated repulsion of cells / regulation of protein localization to plasma membrane / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / positive regulation of double-strand break repair via homologous recombination / RHO GTPases activate IQGAPs / EPHB-mediated forward signaling / substantia nigra development / receptor-mediated endocytosis / axonogenesis / negative regulation of protein binding / positive regulation of cytokine production / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / 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 / tau protein binding / B-WICH complex positively regulates rRNA expression / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / kinetochore / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / nucleosome / actin cytoskeleton / lamellipodium / Clathrin-mediated endocytosis / presynapse
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
Actin, cytoplasmic 1 / C-type lectin domain family 9 member A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle 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 21, 2014-
Header (metadata) releaseJan 21, 2015-
Map releaseMay 27, 2015-
UpdateJun 3, 2015-
Current statusJun 3, 2015Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.838
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.838
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j82
  • Surface level: 0.838
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6102.gif

Downloads & links

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Map

FileDownload / File: emd_6102.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of DNGR1 in complex with F-actin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 100 pix.
= 137. Å		1.37 Å/pix.
x 100 pix.
= 137. Å		1.37 Å/pix.
x 100 pix.
= 137. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.838 / Movie #1: 0.838
Minimum - Maximum-4.13731623 - 5.36457253
Average (Standard dev.)0.15745416 (±0.67706984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 137.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z137.000137.000137.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-4.1375.3650.157

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Supplemental data

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Sample components

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Entire : F-actin complexed with mouse DNGR-1 extracellular domain

EntireName: F-actin complexed with mouse DNGR-1 extracellular domain
Components
  • Sample: F-actin complexed with mouse DNGR-1 extracellular domain
  • Protein or peptide: DNGR-1

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Supramolecule #1000: F-actin complexed with mouse DNGR-1 extracellular domain

SupramoleculeName: 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

MacromoleculeName: DNGR-1 / type: protein_or_peptide / ID: 1 / Name.synonym: CLEC9A / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 25mM Hepes buffer (pH 7.5), 100mM KCl, 1mM MgCl2, 1mM ATP
GridDetails: R0.6/1.0, Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureMin: 50 K / Max: 60 K / Average: 55 K
Specialist opticsEnergy filter - Name: JEOL Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateDec 10, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 774 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

CTF correctionDetails: Each Particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: OTHER / Software - Name: Spider, EMAN / Number images used: 73608

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Atomic model buiding 1

Initial modelPDB ID:

3j82


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Spider, EMAN
DetailsSingle particle--Applied symmetry: C1
RefinementSpace: REAL
Output model

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

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