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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: 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 / 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 / positive regulation of mast cell cytokine production / interleukin-6 biosynthetic process / 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 / cellular response to mechanical stimulus / T cell receptor signaling pathway / 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
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 4.9 Å resolution
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
Validation ReportPDB-ID: 6gk2

SummaryFull reportAbout validation report
DateDeposition: May 18, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Oct 31, 2018 / Last update: Oct 31, 2018

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Structure visualization

Movie
  • Colored surface
  • 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

Fileemd_0013.map.gz (map file in CCP4 format, 96101 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.002 Å
Density
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-3.856203 - 7.497551
Average (Standard dev.)0.019812632 (0.63959557)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions310310250
Origin-155.0-155.0-125.0
Limit154.0154.0124.0
Spacing310310250
CellA: 310.62 Å / B: 310.62 Å / C: 250.5 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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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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Atomic model buiding

Output model

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