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Yorodumi- EMDB-0013: Helical reconstruction of BCL10 CARD and MALT1 DEATH DOMAIN complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0013 | |||||||||
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Title | Helical reconstruction of BCL10 CARD and MALT1 DEATH DOMAIN complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of lymphotoxin A production / polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / antifungal innate immune response / protein kinase B binding / response to fungus / T cell apoptotic process ...positive regulation of lymphotoxin A production / polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / antifungal innate immune response / protein kinase B binding / response to fungus / 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 / CLEC7A/inflammasome pathway / positive regulation of extrinsic apoptotic signaling pathway / nuclear export / response to food / non-canonical NF-kappaB signal transduction / toll-like receptor signaling pathway / B cell activation / positive regulation of T cell receptor signaling pathway / cytoplasmic microtubule / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / small molecule binding / positive regulation of phosphorylation / general transcription initiation factor binding / immunological synapse / NF-kappaB binding / immunoglobulin mediated immune response / cellular defense response / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / 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 / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / fibrillar center / defense response / FCERI mediated NF-kB activation / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / positive regulation of T cell activation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of NF-kappaB transcription factor activity / peptidase activity / protein-macromolecule adaptor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / protease binding / cellular response to lipopolysaccharide / regulation of apoptotic process / transcription coactivator activity / adaptive immune response / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / membrane raft / positive regulation of apoptotic process / cysteine-type endopeptidase activity / innate immune response / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Schlauderer F / Desfosses A / Gutsche I / Hopfner KP / Lammens K | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Molecular architecture and regulation of BCL10-MALT1 filaments. Authors: Florian Schlauderer / Thomas Seeholzer / Ambroise Desfosses / Torben Gehring / Mike Strauss / Karl-Peter Hopfner / Irina Gutsche / Daniel Krappmann / Katja Lammens / Abstract: The CARD11-BCL10-MALT1 (CBM) complex triggers the adaptive immune response in lymphocytes and lymphoma cells. CARD11/CARMA1 acts as a molecular seed inducing BCL10 filaments, but the integration of ...The CARD11-BCL10-MALT1 (CBM) complex triggers the adaptive immune response in lymphocytes and lymphoma cells. CARD11/CARMA1 acts as a molecular seed inducing BCL10 filaments, but the integration of MALT1 and the assembly of a functional CBM complex has remained elusive. Using cryo-EM we solved the helical structure of the BCL10-MALT1 filament. The structural model of the filament core solved at 4.9 Å resolution identified the interface between the N-terminal MALT1 DD and the BCL10 caspase recruitment domain. The C-terminal MALT1 Ig and paracaspase domains protrude from this core to orchestrate binding of mediators and substrates at the filament periphery. Mutagenesis studies support the importance of the identified BCL10-MALT1 interface for CBM complex assembly, MALT1 protease activation and NF-κB signaling in Jurkat and primary CD4 T-cells. Collectively, we present a model for the assembly and architecture of the CBM signaling complex and how it functions as a signaling hub in T-lymphocytes. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0013.map.gz | 66.7 MB | EMDB map data format | |
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Header (meta data) | emd-0013-v30.xml emd-0013.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0013_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_0013.png | 274.1 KB | ||
Others | emd_0013_half_map_1.map.gz emd_0013_half_map_2.map.gz | 46 MB 46 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0013 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0013 | HTTPS FTP |
-Validation report
Summary document | emd_0013_validation.pdf.gz | 417.5 KB | Display | EMDB validaton report |
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Full document | emd_0013_full_validation.pdf.gz | 416.3 KB | Display | |
Data in XML | emd_0013_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0013 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0013 | HTTPS FTP |
-Related structure data
Related structure data | 6gk2MC 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_0013.map.gz / Format: CCP4 / Size: 91.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.002 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Unmasked, unfiltered, helically symmetrized half map 2
File | emd_0013_half_map_1.map | ||||||||||||
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Annotation | Unmasked, unfiltered, helically symmetrized half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unmasked, unfiltered, helically symmetrized half map 1
File | emd_0013_half_map_2.map | ||||||||||||
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Annotation | Unmasked, unfiltered, helically symmetrized half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of BCL10 CARD and MALT1 DEATH DOMAIN
Entire | Name: Complex of BCL10 CARD and MALT1 DEATH DOMAIN |
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Components |
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-Supramolecule #1: Complex of BCL10 CARD and MALT1 DEATH DOMAIN
Supramolecule | Name: Complex of BCL10 CARD and MALT1 DEATH DOMAIN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 104 kDa/nm |
-Macromolecule #1: B-cell lymphoma/leukemia 10
Macromolecule | Name: B-cell lymphoma/leukemia 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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 |
-Macromolecule #2: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Macromolecule | Name: Mucosa-associated lymphoid tissue lymphoma translocation protein 1 type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.401128 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: LNRLREPLLR RLSELLDQAP EGRGWRRLAE LAGSRGRLRL SCLDLEQCSL KVLEPEGSPS LCLLKLMGEK GCTVTELSDF LQAMEHTEV LQL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 99.6 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |