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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 / homologyImmunoglobulin subtype 2 / CLEC7A/inflammasome pathway / CARD caspase recruitment domain profile. / Immunoglobulin subtype / Caspase recruitment domain / Ig-like domain profile. / MALT1, death domain / Immunoglobulin-like domain superfamily / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / Activation of NF-kappaB in B cells ...Immunoglobulin subtype 2 / CLEC7A/inflammasome pathway / CARD caspase recruitment domain profile. / Immunoglobulin subtype / Caspase recruitment domain / Ig-like domain profile. / MALT1, death domain / Immunoglobulin-like domain superfamily / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / Activation of NF-kappaB in B cells / Downstream TCR signaling / B-cell lymphoma/leukemia 10/E10 / Caspase family p20 domain profile. / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Caspase-like domain superfamily / Immunoglobulin-like domain / CARD domain / Peptidase C14, p20 domain / E3 ubiquitin ligases ubiquitinate target proteins / Immunoglobulin-like fold / Death-like domain superfamily / Immunoglobulin domain / interleukin-6 biosynthetic process / positive regulation of mast cell cytokine production / lymphotoxin A biosynthetic process / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / T cell apoptotic process / protein kinase B binding / nuclear export / response to fungus / positive regulation of interleukin-8 biosynthetic process / B cell apoptotic process / response to food / positive regulation of T cell activation / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of mature B cell apoptotic process / cell death / activation of NF-kappaB-inducing kinase activity / immunoglobulin mediated immune response / immunological synapse / positive regulation of interleukin-2 production / T cell proliferation / cytoplasmic microtubule / NF-kappaB binding / toll-like receptor signaling pathway / cellular defense response / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein ubiquitination / neural tube closure / Cysteine proteases / positive regulation of phosphorylation / fibrillar center / defense response / I-kappaB kinase/NF-kappaB signaling / kinase binding / protein heterooligomerization / protein self-association / stimulatory C-type lectin receptor signaling pathway / positive regulation of T cell cytokine production / response to molecule of bacterial origin / Fc-epsilon receptor signaling pathway / ubiquitin-protein transferase activity / T cell receptor signaling pathway / cellular response to mechanical stimulus / adaptive immune response / lysosome / protein complex oligomerization / peptidase activity / protein homooligomerization / positive regulation of I-kappaB kinase/NF-kappaB signaling / cysteine-type endopeptidase activity / protein ubiquitination / transcription coactivator activity / protein C-terminus binding / regulation of apoptotic process / protease binding / positive regulation of NF-kappaB transcription factor activity / membrane raft / positive regulation of apoptotic process / transcription factor binding / ubiquitin protein ligase binding / proteolysis / nucleolus / innate immune response / protein kinase binding / positive regulation of transcription, DNA-templated / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / identical protein binding / nucleus / cytosol / cytoplasm / B-cell lymphoma/leukemia 10 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4.9 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 18, 2018 / Release: Oct 31, 2018

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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
Polyers23,0162
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)1220
ΔGint (kcal/M)-2
Surface area (Å2)12980
MethodPISA

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Components

#1: Protein/peptide B-cell lymphoma/leukemia 10 / 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: (gene. exp.) Homo sapiens (human) / Gene: BCL10, CIPER, CLAP / Production host: Escherichia coli (E. coli) / References: UniProt: O95999
#2: Protein/peptide Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT lymphoma-associated translocation / Paracaspase


Mass: 10401.128 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UDY8, Cysteine proteases

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of BCL10 CARD and MALT1 DEATH DOMAIN / Type: COMPLEX / Entity ID: 1, 2 / 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
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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 deg. / Axial rise/subunit: 5.082 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 25776
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 9600 / Symmetry type: HELICAL

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