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- PDB-4i16: Crystal structure of CARMA1 CARD -

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Basic information

Entry
Database: PDB / ID: 4i16
TitleCrystal structure of CARMA1 CARD
ComponentsCaspase recruitment domain-containing protein 11
KeywordsSIGNALING PROTEIN / CBM complex / Helix bundle / scaffold protein / BCL10 and MALT1 binding / Phosphorylation
Function / homology
Function and homology information


interleukin-2 production / immunoglobulin production / lymphocyte activation / thymic T cell selection / CBM complex / regulation of B cell differentiation / Activation of NF-kappaB in B cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Downstream TCR signaling ...interleukin-2 production / immunoglobulin production / lymphocyte activation / thymic T cell selection / CBM complex / regulation of B cell differentiation / Activation of NF-kappaB in B cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Downstream TCR signaling / TORC1 signaling / CARD domain binding / regulation of T cell differentiation / positive regulation of T cell receptor signaling pathway / B cell proliferation / immunological synapse / homeostasis of number of cells / regulation of immune response / canonical NF-kappaB signal transduction / positive regulation of T cell proliferation / positive regulation of B cell proliferation / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / B cell differentiation / positive regulation of T cell activation / positive regulation of NF-kappaB transcription factor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / membrane raft / signal transduction / plasma membrane / cytoplasm
Similarity search - Function
Caspase recruitment domain-containing protein 11 / 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 ...Caspase recruitment domain-containing protein 11 / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.751 Å
AuthorsLi, S. / Yang, X. / Shen, Y.
CitationJournal: Plos One / Year: 2012
Title: Structural insights into the assembly of CARMA1 and BCL10
Authors: Li, S. / Yang, X. / Shao, J. / Shen, Y.
History
DepositionNov 20, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,2415
Polymers10,8561
Non-polymers3844
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.285, 82.285, 82.285
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-346-

HOH

21A-363-

HOH

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Components

#1: Protein Caspase recruitment domain-containing protein 11


Mass: 10856.454 Da / Num. of mol.: 1 / Fragment: N-TERMINAL CARD DOMAIN, residues 18-110 / Mutation: E18A, E20A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Card11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CIS0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.5
Details: 1.6M MgSO4, 0.1M MES, pH 6.5, LIQUID DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U11.5418
SYNCHROTRONSSRF BL17U20.9795
Detector
TypeIDDetectorDateDetails
RAYONIX MX-2251CCDMay 4, 2010mirrors
RAYONIX MX-2252CCDJul 21, 2010mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97951
ReflectionResolution: 1.75→21.992 Å / Num. all: 18504 / Num. obs: 16403 / % possible obs: 88.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.19 Å2
Reflection shellResolution: 1.75→1.84 Å / % possible all: 64.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.751→21.992 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8238 / SU ML: 0.23 / σ(F): 0 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.232 456 4.81 %RANDOM
Rwork0.1922 ---
all0.1942 9943 --
obs0.1942 9487 94.05 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.401 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso max: 150.02 Å2 / Biso mean: 25.8068 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.751→21.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms739 0 20 89 848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007771
X-RAY DIFFRACTIONf_angle_d1.0141046
X-RAY DIFFRACTIONf_chiral_restr0.078112
X-RAY DIFFRACTIONf_plane_restr0.006131
X-RAY DIFFRACTIONf_dihedral_angle_d16.517290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7507-2.00390.2951220.22652551267382
2.0039-2.52420.20551620.16643136329899
2.5242-21.99330.23221720.197133443516100
Refinement TLS params.Method: refined / Origin x: 7.2506 Å / Origin y: 0.3862 Å / Origin z: -20.4388 Å
111213212223313233
T0.0911 Å20.0075 Å20.0063 Å2-0.0927 Å20.0097 Å2--0.1248 Å2
L0.1859 °2-0.0635 °2-0.0454 °2-0.8771 °2-0.2445 °2--0.7008 °2
S-0.0329 Å °-0.0102 Å °0.0453 Å °-0.0512 Å °0.0072 Å °-0.0779 Å °-0.0463 Å °0.0113 Å °0.0181 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA20 - 109
2X-RAY DIFFRACTION1ALLA201 - 204
3X-RAY DIFFRACTION1ALLA301 - 389

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