[English] 日本語
Yorodumi
- EMDB-27100: Cryo-EM structure of BCL10 CARD - MALT1 DD filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27100
TitleCryo-EM structure of BCL10 CARD - MALT1 DD filament
Map dataCryoEM structure BCL10 CARD-MALT1
Sample
  • Complex: filament
    • Protein or peptide: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
    • Protein or peptide: B-cell lymphoma/leukemia 10
Keywordsfilament / CBM complex / IMMUNE SYSTEM
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 / CBM complex / regulation of T cell receptor signaling pathway / protein kinase B binding / antifungal innate immune response / response to fungus / CARD domain binding ...positive regulation of lymphotoxin A production / polkadots / 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 / antifungal innate immune response / response to fungus / CARD domain binding / positive regulation of mast cell cytokine production / T cell apoptotic process / negative regulation of mature B cell apoptotic process / CLEC7A/inflammasome pathway / B cell apoptotic process / programmed cell death / nuclear export / non-canonical NF-kappaB signal transduction / positive regulation of extrinsic apoptotic signaling pathway / toll-like receptor signaling pathway / response to food / small molecule binding / positive regulation of T cell receptor signaling pathway / B cell activation / immunoglobulin mediated immune response / general transcription initiation factor binding / immunological synapse / positive regulation of phosphorylation / NF-kappaB binding / endopeptidase activator activity / cellular defense response / T cell proliferation / cytoplasmic microtubule / signaling adaptor activity / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / positive regulation of interleukin-8 production / neural tube closure / apoptotic signaling pathway / Activation of NF-kappaB in B cells / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / defense response / positive regulation of T cell cytokine production / protein homooligomerization / positive regulation of T cell activation / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / fibrillar center / ubiquitin-protein transferase activity / Downstream TCR signaling / peptidase activity / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to lipopolysaccharide / protease binding / regulation of apoptotic process / endopeptidase activity / protein-macromolecule adaptor activity / adaptive immune response / transcription coactivator activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / membrane raft / innate immune response / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / proteolysis / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 ...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: 4.3 Å
AuthorsDavid L / Wu H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cancer Discov / Year: 2022
Title: BCL10 Mutations Define Distinct Dependencies Guiding Precision Therapy for DLBCL.
Authors: Min Xia / Liron David / Matt Teater / Johana Gutierrez / Xiang Wang / Cem Meydan / Andrew Lytle / Graham W Slack / David W Scott / Ryan D Morin / Ozlem Onder / Kojo S J Elenitoba-Johnson / ...Authors: Min Xia / Liron David / Matt Teater / Johana Gutierrez / Xiang Wang / Cem Meydan / Andrew Lytle / Graham W Slack / David W Scott / Ryan D Morin / Ozlem Onder / Kojo S J Elenitoba-Johnson / Nahuel Zamponi / Leandro Cerchietti / Tianbao Lu / Ulrike Philippar / Lorena Fontan / Hao Wu / Ari M Melnick /
Abstract: Activated B cell-like diffuse large B-cell lymphomas (ABC-DLBCL) have unfavorable outcomes and chronic activation of CARD11-BCL10-MALT1 (CBM) signal amplification complexes that form due to ...Activated B cell-like diffuse large B-cell lymphomas (ABC-DLBCL) have unfavorable outcomes and chronic activation of CARD11-BCL10-MALT1 (CBM) signal amplification complexes that form due to polymerization of BCL10 subunits, which is affected by recurrent somatic mutations in ABC-DLBCLs. Herein, we show that BCL10 mutants fall into at least two functionally distinct classes: missense mutations of the BCL10 CARD domain and truncation of its C-terminal tail. Truncating mutations abrogated a motif through which MALT1 inhibits BCL10 polymerization, trapping MALT1 in its activated filament-bound state. CARD missense mutations enhanced BCL10 filament formation, forming glutamine network structures that stabilize BCL10 filaments. Mutant forms of BCL10 were less dependent on upstream CARD11 activation and thus manifested resistance to BTK inhibitors, whereas BCL10 truncating but not CARD mutants were hypersensitive to MALT1 inhibitors. Therefore, BCL10 mutations are potential biomarkers for BTK inhibitor resistance in ABC-DLBCL, and further precision can be achieved by selecting therapy based on specific biochemical effects of distinct mutation classes.
SIGNIFICANCE: ABC-DLBCLs feature frequent mutations of signaling mediators that converge on the CBM complex. We use structure-function approaches to reveal that BCL10 mutations fall into two distinct ...SIGNIFICANCE: ABC-DLBCLs feature frequent mutations of signaling mediators that converge on the CBM complex. We use structure-function approaches to reveal that BCL10 mutations fall into two distinct biochemical classes. Both classes confer resistance to BTK inhibitors, whereas BCL10 truncations confer hyperresponsiveness to MALT1 inhibitors, providing a road map for precision therapies in ABC-DLBCLs. See related commentary by Phelan and Oellerich, p. 1844. This article is highlighted in the In This Issue feature, p. 1825.
History
DepositionMay 25, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27100.png

Downloads & links

-
Map

FileDownload / File: emd_27100.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure BCL10 CARD-MALT1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 330 pix.
= 363.627 Å		1.1 Å/pix.
x 330 pix.
= 363.627 Å		1.1 Å/pix.
x 330 pix.
= 363.627 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1019 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.017832788 - 1.995209
Average (Standard dev.)0.005064691 (±0.050215486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 363.62698 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half2 map

Fileemd_27100_half_map_1.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half1 map

Fileemd_27100_half_map_2.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : filament

EntireName: filament
Components
  • Complex: filament
    • Protein or peptide: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
    • Protein or peptide: B-cell lymphoma/leukemia 10

-
Supramolecule #1: filament

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

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

MacromoleculeName: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.615389 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
TLNRLREPLL RRLSELLDQA PEGRGWRRLA ELAGSRGRLR LSCLDLEQCS LKVLEPEGSP SLCLLKLMGE KGCTVTELSD FLQAMEHTE VLQLL

UniProtKB: Mucosa-associated lymphoid tissue lymphoma translocation protein 1

-
Macromolecule #2: B-cell lymphoma/leukemia 10

MacromoleculeName: B-cell lymphoma/leukemia 10 / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.614566 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
EEDLTEVKKD ALENLRVYLC EKIIAERHFD HLRAKKILSR EDTEEISCRT SSRKRAGKLL DYLQENPKGL DTLVESIRRE KTQNFLIQK ITDEVLKLRN IKLEHLK

UniProtKB: B-cell lymphoma/leukemia 10

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMTristrizma base
150.0 mMNaClSodium Chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 700 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 2.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 47000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 23000
Startup modelType of model: EMDB MAP
EMDB ID:

7314

Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more