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- PDB-9avm: Crystal Structure of CARD9 coiled-coil K156-K214 -

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Basic information

Entry
Database: PDB / ID: 9avm
TitleCrystal Structure of CARD9 coiled-coil K156-K214
ComponentsCaspase recruitment domain-containing protein 9
KeywordsIMMUNE SYSTEM / Adapter protein
Function / homology
Function and homology information


regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / response to peptidoglycan / antifungal innate immune response / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of T-helper 17 type immune response / neutrophil mediated immunity / positive regulation of innate immune response ...regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / response to peptidoglycan / antifungal innate immune response / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of T-helper 17 type immune response / neutrophil mediated immunity / positive regulation of innate immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of macrophage cytokine production / response to aldosterone / positive regulation of interleukin-17 production / response to exogenous dsRNA / response to muramyl dipeptide / immunoglobulin mediated immune response / regulation of immune response / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / positive regulation of cytokine production / positive regulation of JNK cascade / apoptotic signaling pathway / NOD1/2 Signaling Pathway / protein homooligomerization / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / regulation of apoptotic process / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / protein homodimerization activity / protein-containing complex / metal ion binding / identical protein 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: 1.79 Å
AuthorsRaymond, D.D. / Lemke, C.T.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Human genetics guides the discovery of novel CARD9 inhibitors with anti-inflammatory activity in vitro as well as in vivo
Authors: Raymond, D.D.
History
DepositionMar 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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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 9
B: Caspase recruitment domain-containing protein 9
C: Caspase recruitment domain-containing protein 9
D: Caspase recruitment domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)28,5564
Polymers28,5564
Non-polymers00
Water1,910106
1
A: Caspase recruitment domain-containing protein 9
B: Caspase recruitment domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)14,2782
Polymers14,2782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-20 kcal/mol
Surface area8350 Å2
MethodPISA
2
C: Caspase recruitment domain-containing protein 9
D: Caspase recruitment domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)14,2782
Polymers14,2782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-26 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.330, 48.830, 55.630
Angle α, β, γ (deg.)71.41, 79.27, 77.05
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 7139.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H257
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 8-14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→26.43 Å / Num. obs: 23908 / % possible obs: 96 % / Redundancy: 2.03 % / CC1/2: 0.997 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.06 / Net I/σ(I): 9.72
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.79-1.90.5238780.7010.7121
1.9-2.030.3436000.7940.4671
2.03-2.190.15833360.9440.2171
2.19-2.390.10230130.9710.141
2.39-2.670.06128850.9890.0831
2.67-3.080.04525130.9930.0611
3.08-3.760.03520860.9940.0481
3.76-5.270.03216540.9960.0431
5.27-26.40.039430.9970.041

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→26.43 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2923 1196 5 %RANDOM
Rwork0.2418 ---
obs0.2443 23908 96.2 %-
Displacement parametersBiso mean: 41.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.313 Å2-1.4392 Å20.6101 Å2
2--2.1284 Å28.1484 Å2
3----2.4414 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.79→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 0 106 1971
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081871HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822473HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d783SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes334HARMONIC5
X-RAY DIFFRACTIONt_it1871HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion18.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion223SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1612SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.8 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2391 -5.01 %
Rwork0.2678 455 -
all0.2665 479 -
obs--92.15 %

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