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- PDB-4lwd: Human CARMA1 CARD domain -

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Basic information

Entry
Database: PDB / ID: 4lwd
TitleHuman CARMA1 CARD domain
ComponentsCaspase recruitment domain-containing protein 11
KeywordsSIGNALING PROTEIN / death domain / Bcl10
Function / homology
Function and homology information


thymic T cell selection / regulation of B cell differentiation / CBM complex / GMP kinase activity / CARD domain binding / CD4-positive, alpha-beta T cell proliferation / TORC1 signaling / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell differentiation / positive regulation of T cell receptor signaling pathway ...thymic T cell selection / regulation of B cell differentiation / CBM complex / GMP kinase activity / CARD domain binding / CD4-positive, alpha-beta T cell proliferation / TORC1 signaling / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell differentiation / positive regulation of T cell receptor signaling pathway / B cell proliferation / homeostasis of number of cells / immunological synapse / canonical NF-kappaB signal transduction / T cell costimulation / positive regulation of B cell proliferation / positive regulation of interleukin-2 production / B cell differentiation / Activation of NF-kappaB in B cells / positive regulation of NF-kappaB transcription factor activity / protein homooligomerization / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Downstream TCR signaling / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / membrane raft / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CARD11, CARD domain / Death Domain, Fas / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily / PDZ superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Caspase recruitment domain-containing protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.792 Å
AuthorsZheng, C. / 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, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase recruitment domain-containing protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6985
Polymers11,3861
Non-polymers3124
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Caspase recruitment domain-containing protein 11
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)70,19130
Polymers68,3166
Non-polymers1,87524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_555-y+3/4,-x+3/4,-z+3/41
crystal symmetry operation19_555-x+3/4,-z+3/4,-y+3/41
crystal symmetry operation24_555-z+3/4,-y+3/4,-x+3/41
Buried area9850 Å2
ΔGint-333 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.045, 82.045, 82.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-312-

HOH

31A-341-

HOH

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Components

#1: Protein Caspase recruitment domain-containing protein 11 / CARD-containing MAGUK protein 1 / Carma 1


Mass: 11385.998 Da / Num. of mol.: 1 / Fragment: CARD domain residues 18-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD11, CARMA1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9BXL7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: It was crystallized by mixing 1 to l protein (10 mg/ml in 20 mM Tris at pH 8.0, 150 mM NaCl, and 5 mM DTT) with 1 to l of the reservoir solution containing 1.4 M MgSO4 and 100 mM MES at pH 6. ...Details: It was crystallized by mixing 1 to l protein (10 mg/ml in 20 mM Tris at pH 8.0, 150 mM NaCl, and 5 mM DTT) with 1 to l of the reservoir solution containing 1.4 M MgSO4 and 100 mM MES at pH 6.5 in a hanging drop vapor diffusion system at 20 oC., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.792→25.945 Å / Num. obs: 9328 / Observed criterion σ(F): 1.36 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.7921-2.05131100
2.0513-2.58411100
2.5841-25.9476199

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.792→25.945 Å / SU ML: 0.46 / σ(F): 1.36 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 466 5 %Random
Rwork0.1986 ---
obs0.1997 9328 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.146 Å2 / ksol: 0.449 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.792→25.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 16 60 820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007772
X-RAY DIFFRACTIONf_angle_d1.0321046
X-RAY DIFFRACTIONf_dihedral_angle_d14.637294
X-RAY DIFFRACTIONf_chiral_restr0.077112
X-RAY DIFFRACTIONf_plane_restr0.005132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7921-2.05130.28041510.23552881X-RAY DIFFRACTION100
2.0513-2.58410.22511540.17072914X-RAY DIFFRACTION100
2.5841-25.94760.2111610.20293067X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9524-2.08270.98934.2694-1.80894.59750.02210.0375-0.1971-0.0972-0.0383-0.17780.27790.16550.04310.1659-0.038-0.02030.0609-0.01230.173150.743839.823921.4735
26.88644.9837-5.9083.72-4.36695.6107-0.2710.58820.2117-0.34450.37680.47590.2388-0.53640.01690.1616-0.03430.00750.2091-0.01690.263437.710741.103516.8221
35.3502-2.29595.32815.8087-3.40595.55970.2089-1.4006-1.00290.66350.97360.740.5705-2.3012-0.46830.4286-0.0754-0.00690.6160.18210.372242.978433.856530.9311
45.15822.0555-0.51645.4011.95937.62710.00980.312-0.1017-0.06530.056-0.1375-0.02690.0317-0.06770.06990.0263-0.00470.10070.02140.151149.559742.105916.0132
56.48450.34462.25596.65871.31627.4868-0.1414-0.04690.4760.08290.0573-1.3969-0.43691.39680.05190.2035-0.0439-0.02230.25280.05920.402160.20745.837523.2115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 21:48)
2X-RAY DIFFRACTION2chain 'A' and (resseq 49:61)
3X-RAY DIFFRACTION3chain 'A' and (resseq 62:73)
4X-RAY DIFFRACTION4chain 'A' and (resseq 74:98)
5X-RAY DIFFRACTION5chain 'A' and (resseq 99:110)

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