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- PDB-6e28: The CARD9 CARD domain-swapped dimer -

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Basic information

Entry
Database: PDB / ID: 6.0E+28
TitleThe CARD9 CARD domain-swapped dimer
ComponentsCaspase recruitment domain-containing protein 9
KeywordsSIGNALING PROTEIN / CARD / innate immunity
Function / homology
Function and homology information


regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / antifungal innate immune response / response to peptidoglycan / positive regulation of stress-activated MAPK cascade / CARD domain binding / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / positive regulation of innate immune response ...regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / antifungal innate immune response / response to peptidoglycan / positive regulation of stress-activated MAPK cascade / CARD domain binding / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / positive regulation of innate immune response / positive regulation of T-helper 17 type immune response / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of macrophage cytokine production / response to aldosterone / response to exogenous dsRNA / positive regulation of interleukin-17 production / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / response to muramyl dipeptide / immunoglobulin mediated immune response / positive regulation of chemokine production / JNK cascade / positive regulation of cytokine production / positive regulation of JNK cascade / NOD1/2 Signaling Pathway / protein homooligomerization / CLEC7A (Dectin-1) signaling / positive regulation of interleukin-6 production / : / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / protein homodimerization activity / protein-containing complex / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CARD9, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Caspase recruitment domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsHolliday, M.J. / Ferrao, R. / Boenig, G. / Deuber, E.C. / Fairbrother, W.J.
CitationJournal: J Biol Chem / Year: 2018
Title: Picomolar zinc binding modulates formation of Bcl10-nucleating assemblies of the caspase recruitment domain (CARD) of CARD9.
Authors: Michael J Holliday / Ryan Ferrao / Gladys de Leon Boenig / Alberto Estevez / Elizabeth Helgason / Alexis Rohou / Erin C Dueber / Wayne J Fairbrother /
Abstract: The caspase recruitment domain-containing protein 9 (CARD9)-B-cell lymphoma/leukemia 10 (Bcl10) signaling axis is activated in myeloid cells during the innate immune response to a variety of diverse ...The caspase recruitment domain-containing protein 9 (CARD9)-B-cell lymphoma/leukemia 10 (Bcl10) signaling axis is activated in myeloid cells during the innate immune response to a variety of diverse pathogens. This signaling pathway requires a critical caspase recruitment domain (CARD)-CARD interaction between CARD9 and Bcl10 that promotes downstream activation of factors, including NF-κB and the mitogen-activated protein kinase (MAPK) p38. Despite these insights, CARD9 remains structurally uncharacterized, and little mechanistic understanding of its regulation exists. We unexpectedly found here that the CARD in CARD9 binds to Zn with picomolar affinity-a concentration comparable with the levels of readily accessible Zn in the cytosol. NMR solution structures of the CARD9-CARD in the apo and Zn-bound states revealed that Zn has little effect on the ground-state structure of the CARD; yet the stability of the domain increased considerably upon Zn binding, with a concomitant reduction in conformational flexibility. Moreover, Zn binding inhibited polymerization of the CARD9-CARD into helical assemblies. Here, we also present a 20-Å resolution negative-stain EM (NS-EM) structure of these filamentous assemblies and show that they adopt a similar helical symmetry as reported previously for filaments of the Bcl10 CARD. Using both bulk assays and direct NS-EM visualization, we further show that the CARD9-CARD assemblies can directly template and thereby nucleate Bcl10 polymerization, a capacity considered critical to propagation of the CARD9-Bcl10 signaling cascade. Our findings indicate that CARD9 is a potential target of Zn-mediated signaling that affects Bcl10 polymerization in innate immune responses.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Caspase recruitment domain-containing protein 9
D: Caspase recruitment domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)22,3812
Polymers22,3812
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-55 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.980, 37.430, 56.880
Angle α, β, γ (deg.)90.00, 101.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Caspase recruitment domain-containing protein 9 / hCARD9


Mass: 11190.732 Da / Num. of mol.: 2 / Fragment: residues 2-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H257
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→43.102 Å / Num. obs: 37569 / % possible obs: 95.6 % / Redundancy: 8.56 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.66
Reflection shellResolution: 1.36→1.394 Å / Num. unique obs: 1934 / % possible all: 70.1

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Processing

Software
NameVersionClassification
PHENIX(1.12-2829)refinement
XDSNov. 1, 2016data reduction
XSCALENov. 1, 2016data scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LWD

4lwd


Resolution: 1.36→43.102 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3
RfactorNum. reflection% reflection
Rfree0.1937 2000 5.33 %
Rwork0.1798 --
obs0.1805 37558 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.36→43.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 0 153 1653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091558
X-RAY DIFFRACTIONf_angle_d1.0112123
X-RAY DIFFRACTIONf_dihedral_angle_d24.887601
X-RAY DIFFRACTIONf_chiral_restr0.077245
X-RAY DIFFRACTIONf_plane_restr0.007271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.3940.3451030.38311831X-RAY DIFFRACTION70
1.394-1.43170.35231280.2982287X-RAY DIFFRACTION87
1.4317-1.47390.28121450.24942573X-RAY DIFFRACTION98
1.4739-1.52140.27841460.2252577X-RAY DIFFRACTION98
1.5214-1.57580.23941450.21722583X-RAY DIFFRACTION98
1.5758-1.63890.22971440.2112579X-RAY DIFFRACTION98
1.6389-1.71350.24241460.20642579X-RAY DIFFRACTION98
1.7135-1.80380.22511470.20592631X-RAY DIFFRACTION99
1.8038-1.91690.23921480.20042618X-RAY DIFFRACTION99
1.9169-2.06490.20511480.18252640X-RAY DIFFRACTION99
2.0649-2.27260.18931480.17752619X-RAY DIFFRACTION99
2.2726-2.60150.17751480.16712638X-RAY DIFFRACTION99
2.6015-3.27740.21281500.18482672X-RAY DIFFRACTION100
3.2774-43.12380.1581540.15512731X-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)
15.19932.0480.2583.3449-1.23031.9312-0.04640.6679-0.21530.0180.25340.1131-0.1904-0.3444-0.20040.19310.0043-0.02510.2323-0.0230.318-14.6869-2.2046-34.7471
26.9234-2.0191-2.29823.18372.62163.55630.0905-0.10430.2577-0.15180.4083-0.5897-0.42580.5043-0.55510.2281-0.05130.01210.233-0.05190.213-2.30787.8938-24.2573
33.99730.065-0.34393.4166-0.16394.2030.2015-0.12710.09460.0391-0.115-0.1422-0.45920.0903-0.0460.1745-0.00540.02210.14-0.01430.10864.861418.1524-6.7858
44.49071.0482-0.74364.15561.6912.64650.1417-0.47620.32830.39330.0931-0.1357-0.24670.1199-0.21240.27460.02710.02340.2301-0.02050.17224.351919.3720.4935
54.3129-0.4624-4.39283.35871.62814.9197-0.19010.1547-0.1762-0.21070.072-0.0455-0.0373-0.06910.1040.2187-0.01230.03520.17080.00650.19455.275914.4163-15.2284
64.18944.72410.38565.5391-0.26612.6332-0.2220.037-0.7802-0.6836-0.2709-0.85630.52060.38010.50170.30450.03260.09760.23710.0340.300412.47278.7156-11.9114
72.25973.55320.32625.47530.6284.443-0.31090.4762-0.5721-0.20690.4474-0.64080.18930.1411-0.03990.2256-0.03820.01940.1948-0.02150.2746-0.97074.2538-12.4863
88.12012.1873-4.86636.8267-3.1953.48570.2837-0.1363-0.03680.1184-0.15580.206-0.4281-0.1861-0.20850.14950.0042-0.0070.1457-0.01250.1659-11.80166.5349-24.9083
96.1462-1.56241.85922.7547-4.47478.29130.15080.1311-0.2730.002-0.0271-0.35490.23960.36430.00330.1910.0364-0.02810.1799-0.04540.2302-3.8241-2.4773-32.7679
103.0973.24123.30784.22325.3978.63370.2616-0.0265-0.50230.3526-0.29140.061.0424-0.0861-0.04860.299-0.0051-0.05030.1969-0.00450.3267-8.419-10.8754-27.8495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'C' and (resid 25 through 53 )
3X-RAY DIFFRACTION3chain 'C' and (resid 54 through 97 )
4X-RAY DIFFRACTION4chain 'D' and (resid 8 through 24 )
5X-RAY DIFFRACTION5chain 'D' and (resid 25 through 36 )
6X-RAY DIFFRACTION6chain 'D' and (resid 37 through 41 )
7X-RAY DIFFRACTION7chain 'D' and (resid 42 through 53 )
8X-RAY DIFFRACTION8chain 'D' and (resid 54 through 71 )
9X-RAY DIFFRACTION9chain 'D' and (resid 72 through 86 )
10X-RAY DIFFRACTION10chain 'D' and (resid 87 through 97 )

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