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- EMDB-7314: Cryo-EM structure of BCL10 CARD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-7314
TitleCryo-EM structure of BCL10 CARD filament
Map dataCryo-EM reconstruction of BCL10 CARD at 4A resolution
Sample
  • Complex: BCL10 CARD
    • Protein or peptide: B-cell lymphoma/leukemia 10
KeywordsCARD / filament / signalosome / helical reconstruction / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of lymphotoxin A production / polkadots / CBM complex / antifungal innate immune response / protein kinase B binding / 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 ...positive regulation of lymphotoxin A production / polkadots / CBM complex / antifungal innate immune response / protein kinase B binding / 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 / positive regulation of extrinsic apoptotic signaling pathway / response to food / toll-like receptor signaling pathway / positive regulation of T cell receptor signaling pathway / non-canonical NF-kappaB signal transduction / 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 / positive regulation of phosphorylation / lipopolysaccharide-mediated signaling pathway / positive regulation of protein ubiquitination / neural tube closure / positive regulation of interleukin-8 production / Activation of NF-kappaB in B cells / protein homooligomerization / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / : / positive regulation of T cell activation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / protease binding / adaptive immune response / lysosome / transcription coactivator activity / positive regulation of apoptotic process / membrane raft / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / protein-containing complex / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
B-cell lymphoma/leukemia 10/E10 / BCL10, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
B-cell lymphoma/leukemia 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsDavid L / Li Y / Ma J / Garner E / Zhang X / Wu H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI089882 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Assembly mechanism of the CARMA1-BCL10-MALT1-TRAF6 signalosome.
Authors: Liron David / Yang Li / Jun Ma / Ethan Garner / Xinzheng Zhang / Hao Wu /
Abstract: The CARMA1-BCL10-MALT1 (CBM) signalosome is a central mediator of T cell receptor and B cell receptor-induced NF-κB signaling that regulates multiple lymphocyte functions. While caspase-recruitment ...The CARMA1-BCL10-MALT1 (CBM) signalosome is a central mediator of T cell receptor and B cell receptor-induced NF-κB signaling that regulates multiple lymphocyte functions. While caspase-recruitment domain (CARD) membrane-associated guanylate kinase (MAGUK) protein 1 (CARMA1) nucleates B cell lymphoma 10 (BCL10) filament formation through interactions between CARDs, mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a paracaspase with structural similarity to caspases, which recruits TNF receptor-associated factor 6 (TRAF6) for K63-linked polyubiquitination. Here we present cryo-electron microscopy (cryo-EM) structure of the BCL10 CARD filament at 4.0-Å resolution. The structure redefines CARD-CARD interactions compared with the previous EM structure determined from a negatively stained sample. Surprisingly, time-lapse confocal imaging shows that BCL10 polymerizes in a unidirectional manner. CARMA1, the BCL10 nucleator, serves as a hub for formation of star-shaped filamentous networks of BCL10 and significantly decreases the lag period of BCL10 polymerization. Cooperative MALT1 interaction with BCL10 filaments observed under EM suggests immediate dimerization of MALT1 in the BCL10 filamentous scaffold. In addition, TRAF6 cooperatively decorates CBM filaments to form higher-order assemblies, likely resulting in all-or-none activation of the downstream pathway. Collectively, these data reveal biophysical mechanisms in the assembly of the CARMA1-BCL10-MALT1-TRAF6 complex for signal transduction.
History
DepositionDec 23, 2017-
Header (metadata) releaseFeb 14, 2018-
Map releaseFeb 14, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0485
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0485
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6bze
  • Surface level: 0.0485
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6bze
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7314.png

Downloads & links

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Map

FileDownload / File: emd_7314.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of BCL10 CARD at 4A resolution
Voxel sizeX=Y=Z: 1.51 Å
Density
Contour LevelBy AUTHOR: 0.0485 / Movie #1: 0.0485
Minimum - Maximum-0.08693058 - 0.1856001
Average (Standard dev.)0.006188636 (±0.020250324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 151.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.511.511.51
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z151.000151.000151.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.0870.1860.006

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Supplemental data

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Sample components

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Entire : BCL10 CARD

EntireName: BCL10 CARD
Components
  • Complex: BCL10 CARD
    • Protein or peptide: B-cell lymphoma/leukemia 10

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Supramolecule #1: BCL10 CARD

SupramoleculeName: BCL10 CARD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 8 / 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

UniProtKB: B-cell lymphoma/leukemia 10

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chlorideSodium Chloride
1.0 mMC9H15O6PTCEP
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK III / Details: 5 second blotting time with force 3.

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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 / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 339 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 103873 / Software - Name: EMAN2
Software - details: EMAN2 e2helixboxer was used to select filament segments
Startup modelType of model: OTHER / Details: Cylinder/negative stained EM model
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -100.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Software - details: phenix refine / Number images used: 39992

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Atomic model buiding 1

Initial modelPDB ID:

2mb9


Chain - Chain ID: A / Chain - Residue range: 10-115 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6bze:
Cryo-EM structure of BCL10 CARD filament

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