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- EMDB-5729: Bcl10 filament -

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Basic information

Entry
Database: EMDB / ID: EMD-5729
TitleBcl10 filament
Map dataIHRSR reconstruction of Bcl10 filament
Sample
  • Sample: Bcl10
  • Protein or peptide: Bcl10
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / negative staining / Resolution: 20.0 Å
AuthorsQiao Q / Yang C / Zheng C / David L / Yu X / Fontan L / Bracken WC / Garcia M / Melnick A / Egelman EH / Wu H
CitationJournal: Mol Cell / Year: 2013
Title: Structural architecture of the CARMA1/Bcl10/MALT1 signalosome: nucleation-induced filamentous assembly.
Authors: Qi Qiao / Chenghua Yang / Chao Zheng / Lorena Fontán / Liron David / Xiong Yu / Clay Bracken / Monica Rosen / Ari Melnick / Edward H Egelman / Hao Wu /
Abstract: The CARMA1/Bcl10/MALT1 (CBM) signalosome mediates antigen receptor-induced NF-κB signaling to regulate multiple lymphocyte functions. While CARMA1 and Bcl10 contain caspase recruitment domains ...The CARMA1/Bcl10/MALT1 (CBM) signalosome mediates antigen receptor-induced NF-κB signaling to regulate multiple lymphocyte functions. While CARMA1 and Bcl10 contain caspase recruitment domains (CARDs), MALT1 is a paracaspase with structural similarity to caspases. Here we show that the reconstituted CBM signalosome is a helical filamentous assembly in which substoichiometric CARMA1 nucleates Bcl10 filaments. Bcl10 filament formation is a highly cooperative process whose threshold is sensitized by oligomerized CARMA1 upon receptor activation. In cells, both cotransfected CARMA1/Bcl10 complex and the endogenous CBM signalosome are filamentous morphologically. Combining crystallography, nuclear magnetic resonance, and electron microscopy, we reveal the structure of the Bcl10 CARD filament and the mode of interaction between CARMA1 and Bcl10. Structure-guided mutagenesis confirmed the observed interfaces in Bcl10 filament assembly and MALT1 activation in vitro and NF-κB activation in cells. These data support a paradigm of nucleation-induced signal transduction with threshold response due to cooperativity and signal amplification by polymerization.
History
DepositionJul 26, 2013-
Header (metadata) releaseMar 19, 2014-
Map releaseMar 19, 2014-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.22
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5729.gif

Downloads & links

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Map

FileDownload / File: emd_5729.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIHRSR reconstruction of Bcl10 filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.16 Å/pix.
x 100 pix.
= 416. Å		4.16 Å/pix.
x 100 pix.
= 416. Å		4.16 Å/pix.
x 100 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.05 / Movie #1: 0.22
Minimum - Maximum-0.26180375 - 0.81234527
Average (Standard dev.)0.00962873 (±0.06774642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.164.164.16
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.2620.8120.010

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Supplemental data

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Sample components

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Entire : Bcl10

EntireName: Bcl10
Components
  • Sample: Bcl10
  • Protein or peptide: Bcl10

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Supramolecule #1000: Bcl10

SupramoleculeName: Bcl10 / type: sample / ID: 1000 / Oligomeric state: helical polymer / Number unique components: 1

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Macromolecule #1: Bcl10

MacromoleculeName: Bcl10 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: unidentified (others)

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

StainingType: NEGATIVE / Details: 1% uranyl acetate
GridDetails: 300 mesh copper grid with thin carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateJan 1, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Bits/pixel: 14
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: OTHER

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Image processing

DetailsThe particles were reconstructed using IHRSR.
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 100.9 °
Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR, Spider

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