+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7314 | |||||||||
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Title | Cryo-EM structure of BCL10 CARD filament | |||||||||
Map data | Cryo-EM reconstruction of BCL10 CARD at 4A resolution | |||||||||
Sample |
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Keywords | CARD / filament / signalosome / helical reconstruction / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of lymphotoxin A production / polkadots / CBM complex / antifungal innate immune response / protein kinase B binding / T cell apoptotic process / positive regulation of mast cell cytokine production / CARD domain binding / programmed cell death / negative regulation of mature B cell apoptotic process ...positive regulation of lymphotoxin A production / polkadots / CBM complex / antifungal innate immune response / protein kinase B binding / T cell apoptotic process / positive regulation of mast cell cytokine production / CARD domain binding / programmed cell death / negative regulation of mature B cell apoptotic process / B cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / response to food / non-canonical NF-kappaB signal transduction / toll-like receptor signaling pathway / positive regulation of T cell receptor signaling pathway / cytoplasmic microtubule / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of phosphorylation / general transcription initiation factor binding / immunological synapse / NF-kappaB binding / immunoglobulin mediated immune response / cellular defense response / lipopolysaccharide-mediated signaling pathway / positive regulation of protein ubiquitination / neural tube closure / positive regulation of interleukin-8 production / Activation of NF-kappaB in B cells / cellular response to mechanical stimulus / protein homooligomerization / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / positive regulation of interleukin-6 production / positive regulation of T cell activation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / protease binding / cellular response to lipopolysaccharide / transcription coactivator activity / adaptive immune response / lysosome / membrane raft / positive regulation of apoptotic process / innate immune response / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | David L / Li Y / Ma J / Garner E / Zhang X / Wu H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Assembly mechanism of the CARMA1-BCL10-MALT1-TRAF6 signalosome. Authors: Liron David / Yang Li / Jun Ma / Ethan Garner / Xinzheng Zhang / Hao Wu / Abstract: The CARMA1-BCL10-MALT1 (CBM) signalosome is a central mediator of T cell receptor and B cell receptor-induced NF-κB signaling that regulates multiple lymphocyte functions. While caspase-recruitment ...The CARMA1-BCL10-MALT1 (CBM) signalosome is a central mediator of T cell receptor and B cell receptor-induced NF-κB signaling that regulates multiple lymphocyte functions. While caspase-recruitment domain (CARD) membrane-associated guanylate kinase (MAGUK) protein 1 (CARMA1) nucleates B cell lymphoma 10 (BCL10) filament formation through interactions between CARDs, mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a paracaspase with structural similarity to caspases, which recruits TNF receptor-associated factor 6 (TRAF6) for K63-linked polyubiquitination. Here we present cryo-electron microscopy (cryo-EM) structure of the BCL10 CARD filament at 4.0-Å resolution. The structure redefines CARD-CARD interactions compared with the previous EM structure determined from a negatively stained sample. Surprisingly, time-lapse confocal imaging shows that BCL10 polymerizes in a unidirectional manner. CARMA1, the BCL10 nucleator, serves as a hub for formation of star-shaped filamentous networks of BCL10 and significantly decreases the lag period of BCL10 polymerization. Cooperative MALT1 interaction with BCL10 filaments observed under EM suggests immediate dimerization of MALT1 in the BCL10 filamentous scaffold. In addition, TRAF6 cooperatively decorates CBM filaments to form higher-order assemblies, likely resulting in all-or-none activation of the downstream pathway. Collectively, these data reveal biophysical mechanisms in the assembly of the CARMA1-BCL10-MALT1-TRAF6 complex for signal transduction. | |||||||||
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_7314.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-7314-v30.xml emd-7314.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_7314.png | 44.2 KB | ||
Filedesc metadata | emd-7314.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7314 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7314 | HTTPS FTP |
-Validation report
Summary document | emd_7314_validation.pdf.gz | 620.3 KB | Display | EMDB validaton report |
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Full document | emd_7314_full_validation.pdf.gz | 619.9 KB | Display | |
Data in XML | emd_7314_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_7314_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7314 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7314 | HTTPS FTP |
-Related structure data
Related structure data | 6bzeMC 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_7314.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of BCL10 CARD at 4A resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.51 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 : BCL10 CARD
Entire | Name: BCL10 CARD |
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Components |
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-Supramolecule #1: BCL10 CARD
Supramolecule | Name: BCL10 CARD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: B-cell lymphoma/leukemia 10
Macromolecule | Name: B-cell lymphoma/leukemia 10 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.614566 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EEDLTEVKKD ALENLRVYLC EKIIAERHFD HLRAKKILSR EDTEEISCRT SSRKRAGKLL DYLQENPKGL DTLVESIRRE KTQNFLIQK ITDEVLKLRN IKLEHLK UniProtKB: B-cell lymphoma/leukemia 10 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK III / Details: 5 second blotting time with force 3. |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 339 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 5.0 Å Applied symmetry - Helical parameters - Δ&Phi: -100.8 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Software - details: phenix refine / Number images used: 39992 |
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Segment selection | Number selected: 103873 / Software - Name: EMAN2 Software - details: EMAN2 e2helixboxer was used to select filament segments |
Startup model | Type of model: OTHER / Details: Cylinder/negative stained EM model |
Final angle assignment | Type: NOT APPLICABLE |