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- EMDB-0013: Helical reconstruction of BCL10 CARD and MALT1 DEATH DOMAIN complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0013
TitleHelical reconstruction of BCL10 CARD and MALT1 DEATH DOMAIN complex
Map data
Sample
  • Complex: Complex of BCL10 CARD and MALT1 DEATH DOMAIN
    • Protein or peptide: B-cell lymphoma/leukemia 10
    • Protein or peptide: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
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 / regulation of T cell receptor signaling pathway / CBM complex / 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 / regulation of T cell receptor signaling pathway / CBM complex / 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 / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / positive regulation of extrinsic apoptotic signaling pathway / response to food / toll-like receptor signaling pathway / B cell activation / positive regulation of T cell receptor signaling pathway / non-canonical NF-kappaB signal transduction / small molecule binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / immunoglobulin mediated immune response / immunological synapse / general transcription initiation factor binding / NF-kappaB binding / canonical NF-kappaB signal transduction / cellular defense response / cytoplasmic microtubule / T cell proliferation / positive regulation of phosphorylation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of protein ubiquitination / positive regulation of interleukin-1 beta production / neural tube closure / positive regulation of interleukin-8 production / Activation of NF-kappaB in B cells / protein homooligomerization / defense response / fibrillar center / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production / FCERI mediated NF-kB activation / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / 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 / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / cellular response to lipopolysaccharide / protease binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / adaptive immune response / lysosome / transcription coactivator activity / positive regulation of apoptotic process / membrane raft / cysteine-type endopeptidase activity / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / protein-containing complex / proteolysis / 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 / Immunoglobulin 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)
Methodhelical reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsSchlauderer F / Desfosses A / Gutsche I / Hopfner KP / 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, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseOct 31, 2018-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gk2
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6gk2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0013.png

Downloads & links

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Map

FileDownload / File: emd_0013.map.gz / Format: CCP4 / Size: 91.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.002 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-3.856203 - 7.497551
Average (Standard dev.)0.019812632 (±0.63959557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-155-155-125
Dimensions310310250
Spacing310310250
CellA: 310.62 Å / B: 310.62 Å / C: 250.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0021.0021.002
M x/y/z310310250
origin x/y/z0.0000.0000.000
length x/y/z310.620310.620250.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-155-155-125
NC/NR/NS310310250
D min/max/mean-3.8567.4980.020

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Supplemental data

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Half map: Unmasked, unfiltered, helically symmetrized half map 2

Fileemd_0013_half_map_1.map
AnnotationUnmasked, unfiltered, helically symmetrized half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked, unfiltered, helically symmetrized half map 1

Fileemd_0013_half_map_2.map
AnnotationUnmasked, unfiltered, helically symmetrized half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of BCL10 CARD and MALT1 DEATH DOMAIN

EntireName: Complex of BCL10 CARD and MALT1 DEATH DOMAIN
Components
  • Complex: Complex of BCL10 CARD and MALT1 DEATH DOMAIN
    • Protein or peptide: B-cell lymphoma/leukemia 10
    • Protein or peptide: Mucosa-associated lymphoid tissue lymphoma translocation protein 1

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Supramolecule #1: Complex of BCL10 CARD and MALT1 DEATH DOMAIN

SupramoleculeName: Complex of BCL10 CARD and MALT1 DEATH DOMAIN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 104 kDa/nm

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Macromolecule #1: B-cell lymphoma/leukemia 10

MacromoleculeName: B-cell lymphoma/leukemia 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.614566 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EEDLTEVKKD ALENLRVYLC EKIIAERHFD HLRAKKILSR EDTEEISCRT SSRKRAGKLL DYLQENPKGL DTLVESIRRE KTQNFLIQK ITDEVLKLRN IKLEHLK

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Macromolecule #2: Mucosa-associated lymphoid tissue lymphoma translocation protein 1

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.401128 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LNRLREPLLR RLSELLDQAP EGRGWRRLAE LAGSRGRLRL SCLDLEQCSL KVLEPEGSPS LCLLKLMGEK GCTVTELSDF LQAMEHTEV LQL

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 99.6 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 25776 / Software - Name: SPRING (ver. 0.86)
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.082 Å
Applied symmetry - Helical parameters - Δ&Phi: -100.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPRING (ver. 0.86) / Number images used: 9600
FSC plot (resolution estimation)

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