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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
SampleComplex of BCL10 CARD and MALT1 DEATH DOMAIN
  • B-cell lymphoma/leukemia 10
  • Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Function / homology
Function and homology information


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 / protein kinase B binding / T cell apoptotic process / nuclear export ...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 / protein kinase B binding / T cell apoptotic process / nuclear export / response to fungus / positive regulation of kinase activity / B cell apoptotic process / CARD domain binding / positive regulation of interleukin-1 beta production / response to food / negative regulation of mature B cell apoptotic process / positive regulation of T cell activation / positive regulation of extrinsic apoptotic signaling pathway / activation of NF-kappaB-inducing kinase activity / immunoglobulin mediated immune response / cell death / positive regulation of interleukin-8 biosynthetic process / B cell activation / immunological synapse / T cell proliferation / response to molecule of bacterial origin / positive regulation of interleukin-2 production / cytoplasmic microtubule / NF-kappaB binding / cellular defense response / toll-like receptor signaling pathway / protein heterooligomerization / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein ubiquitination / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of phosphorylation / lipopolysaccharide-mediated signaling pathway / fibrillar center / neural tube closure / I-kappaB kinase/NF-kappaB signaling / kinase binding / defense response / positive regulation of T cell cytokine production / protein self-association / ubiquitin-protein transferase activity / stimulatory C-type lectin receptor signaling pathway / cellular response to mechanical stimulus / protein complex oligomerization / Fc-epsilon receptor signaling pathway / protein homooligomerization / peptidase activity / positive regulation of I-kappaB kinase/NF-kappaB signaling / regulation of apoptotic process / T cell receptor signaling pathway / adaptive immune response / cysteine-type endopeptidase activity / transcription coactivator activity / lysosome / protein C-terminus binding / protease binding / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / membrane raft / positive regulation of apoptotic process / transcription factor binding / proteolysis / ubiquitin protein ligase binding / innate immune response / protein kinase binding / negative regulation of apoptotic process / positive regulation of transcription, DNA-templated / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / identical protein binding / nucleus / cytosol / cytoplasm
Death-like domain superfamily / Immunoglobulin-like domain / Peptidase C14, p20 domain / BCL10, CARD domain / CARD domain / MALT1 immunoglobulin-like domain / MALT1, death domain / Immunoglobulin subtype 2 / Immunoglobulin-like domain superfamily / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 ...Death-like domain superfamily / Immunoglobulin-like domain / Peptidase C14, p20 domain / BCL10, CARD domain / CARD domain / MALT1 immunoglobulin-like domain / MALT1, death domain / Immunoglobulin subtype 2 / Immunoglobulin-like domain superfamily / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / Immunoglobulin subtype / B-cell lymphoma/leukemia 10/E10 / Caspase-like domain superfamily / Immunoglobulin-like fold
B-cell lymphoma/leukemia 10 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
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-
UpdateOct 31, 2018-
Current statusOct 31, 2018Processing 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 models: PDB-6gk2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 250 pix.
= 250.5 Å
1 Å/pix.
x 310 pix.
= 310.62 Å
1 Å/pix.
x 310 pix.
= 310.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.002 Å
Density
Contour LevelBy AUTHOR: 2. / 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

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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

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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 / Number of components: 3

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Component #1: protein, Complex of BCL10 CARD and MALT1 DEATH DOMAIN

ProteinName: Complex of BCL10 CARD and MALT1 DEATH DOMAIN / Recombinant expression: No
MassExperimental: 104 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, B-cell lymphoma/leukemia 10

ProteinName: B-cell lymphoma/leukemia 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.614566 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Mucosa-associated lymphoid tissue lymphoma translocation...

ProteinName: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.401128 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 5.082 Å / Delta phi: -100.8 %deg;
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 99.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPRING / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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