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- PDB-6gk2: Helical reconstruction of BCL10 CARD and MALT1 DEATH DOMAIN complex -

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Basic information

Entry
Database: PDB / ID: 6gk2
TitleHelical reconstruction of BCL10 CARD and MALT1 DEATH DOMAIN complex
Components
  • B-cell lymphoma/leukemia 10
  • Mucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsIMMUNE SYSTEM / BCL10 / MALT1 / CBM complex / helical reconstruction / cancer / autoimmune disease
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 / protein kinase B binding / antifungal innate immune response / response to fungus / CARD domain binding ...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 / protein kinase B binding / antifungal innate immune response / response to fungus / CARD domain binding / positive regulation of mast cell cytokine production / T cell apoptotic process / negative regulation of mature B cell apoptotic process / CLEC7A/inflammasome pathway / programmed cell death / B cell apoptotic process / nuclear export / non-canonical NF-kappaB signal transduction / positive regulation of extrinsic apoptotic signaling pathway / toll-like receptor signaling pathway / response to food / small molecule binding / positive regulation of T cell receptor signaling pathway / B cell activation / immunoglobulin mediated immune response / general transcription initiation factor binding / immunological synapse / positive regulation of phosphorylation / NF-kappaB binding / endopeptidase activator activity / cellular defense response / T cell proliferation / cytoplasmic microtubule / signaling adaptor activity / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / positive regulation of interleukin-8 production / neural tube closure / apoptotic signaling pathway / Activation of NF-kappaB in B cells / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / defense response / positive regulation of T cell cytokine production / protein homooligomerization / positive regulation of T cell activation / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / fibrillar center / ubiquitin-protein transferase activity / Downstream TCR signaling / peptidase activity / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to lipopolysaccharide / protease binding / protein-macromolecule adaptor activity / regulation of apoptotic process / endopeptidase activity / adaptive immune response / transcription coactivator activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / membrane raft / innate immune response / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / protein-containing complex / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
B-cell lymphoma/leukemia 10/E10 / BCL10, CARD domain / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / : / MALT1 Ig-like domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain ...B-cell lymphoma/leukemia 10/E10 / BCL10, CARD domain / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / : / MALT1 Ig-like domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Immunoglobulin domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
B-cell lymphoma/leukemia 10 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsSchlauderer, F. / Desfosses, A. / Gutsche, I. / Hopfner, K.P. / Lammens, K.
CitationJournal: 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
DepositionMay 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
H: B-cell lymphoma/leukemia 10
F: Mucosa-associated lymphoid tissue lymphoma translocation protein 1


Theoretical massNumber of molelcules
Total (without water)23,0162
Polymers23,0162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1220 Å2
ΔGint-2 kcal/mol
Surface area12980 Å2
MethodPISA

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Components

#1: Protein B-cell lymphoma/leukemia 10 / B-cell CLL/lymphoma 10 / Bcl-10 / CARD-containing molecule enhancing NF-kappa-B / CARD-like ...B-cell CLL/lymphoma 10 / Bcl-10 / CARD-containing molecule enhancing NF-kappa-B / CARD-like apoptotic protein / hCLAP / CED-3/ICH-1 prodomain homologous E10-like regulator / CIPER / Cellular homolog of vCARMEN / cCARMEN / Cellular-E10 / c-E10 / Mammalian CARD-containing adapter molecule E10 / mE10


Mass: 12614.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL10, CIPER, CLAP / Production host: Escherichia coli (E. coli) / References: UniProt: O95999
#2: Protein Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT lymphoma-associated translocation / Paracaspase


Mass: 10401.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of BCL10 CARD and MALT1 DEATH DOMAIN / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 104 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 99.6 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1SPRING0.86particle selection
4CTFFIND3CTF correction
7Cootmodel fitting
12SPRING0.863D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -100.8 ° / Axial rise/subunit: 5.082 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 25776
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9600 / Symmetry type: HELICAL

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