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- PDB-9avn: Crystal Structure of CARD9 coiled-coil K156-K214 bound to Compound 1 -

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Basic information

Entry
Database: PDB / ID: 9avn
TitleCrystal Structure of CARD9 coiled-coil K156-K214 bound to Compound 1
ComponentsCaspase recruitment domain-containing protein 9
KeywordsIMMUNE SYSTEM / Adapter protein
Function / homology
Function and homology information


regulation of interleukin-2 production / host-mediated modulation of intestinal microbiota composition / CBM complex / antifungal innate immune response / response to peptidoglycan / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of T-helper 17 type immune response / response to aldosterone / neutrophil mediated immunity ...regulation of interleukin-2 production / host-mediated modulation of intestinal microbiota composition / CBM complex / antifungal innate immune response / response to peptidoglycan / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of T-helper 17 type immune response / response to aldosterone / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / positive regulation of innate immune response / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of macrophage cytokine production / response to exogenous dsRNA / response to muramyl dipeptide / positive regulation of interleukin-17 production / 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 tumor necrosis factor production / regulation of apoptotic process / defense response to virus / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / 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: 2.726 Å
AuthorsRaymond, D.D. / Lemke, C.T.
Funding support1items
OrganizationGrant numberCountry
Other government
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
E: Caspase recruitment domain-containing protein 9
F: Caspase recruitment domain-containing protein 9
G: Caspase recruitment domain-containing protein 9
H: Caspase recruitment domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,27710
Polymers57,1138
Non-polymers1,1642
Water1267
1
A: Caspase recruitment domain-containing protein 9
B: Caspase recruitment domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8603
Polymers14,2782
Non-polymers5821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-26 kcal/mol
Surface area8680 Å2
MethodPISA
2
C: Caspase recruitment domain-containing protein 9
D: Caspase recruitment domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8603
Polymers14,2782
Non-polymers5821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26 kcal/mol
Surface area8710 Å2
MethodPISA
3
E: Caspase recruitment domain-containing protein 9
F: Caspase recruitment domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)14,2782
Polymers14,2782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-25 kcal/mol
Surface area8530 Å2
MethodPISA
4
G: Caspase recruitment domain-containing protein 9
H: Caspase recruitment domain-containing protein 9


Theoretical massNumber of molelcules
Total (without water)14,2782
Polymers14,2782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-24 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 56.050, 84.300
Angle α, β, γ (deg.)90.00, 97.75, 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: 7139.121 Da / Num. of mol.: 8
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: Chemical ChemComp-A1AG7 / (2P)-2-(1-benzyl-3-phenyl-1H-pyrazol-4-yl)-5-chloro-1-[(1R)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]-1H-1,3-benzimidazole-6-carboxylic acid


Mass: 582.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H32ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.33 Å3/Da / Density % sol: 47.31 %
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: 2.726→83.53 Å / Num. obs: 25922 / % possible obs: 95 % / Redundancy: 1.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.097 / Net I/σ(I): 6.64
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.73-2.80.50720070.6950.6951
2.8-2.870.38218710.7950.5241
2.87-2.960.28318730.8870.391
2.96-3.050.22817830.9050.3151
3.05-3.150.19217370.9330.2641
3.15-3.260.15816320.9450.2161
3.26-3.380.13815830.9610.191
3.38-3.520.11215800.970.1551
3.52-3.680.09314300.9770.1271
3.68-3.860.07713870.9840.1071
3.86-4.060.06213450.9930.0861
4.06-4.310.05912480.9930.0821
4.31-4.610.05411680.9920.0751
4.61-4.980.04411040.9970.0621
4.98-5.450.0459930.9970.0641
5.45-6.10.0679090.9890.0941
6.1-7.040.0518040.9960.0711
7.04-8.620.0416700.9950.0581
8.62-12.190.0355130.9950.051
12.19-83.530.0422850.9930.0591

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.726→83.53 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.409
RfactorNum. reflection% reflectionSelection details
Rfree0.2988 708 5.07 %RANDOM
Rwork0.2743 ---
obs0.2756 13975 98.8 %-
Displacement parametersBiso mean: 68.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.7325 Å20 Å2-5.3756 Å2
2---10.7595 Å20 Å2
3---15.492 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.726→83.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 84 7 3713
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083728HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874943HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1555SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes733HARMONIC5
X-RAY DIFFRACTIONt_it3728HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion21.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion434SEMIHARMONIC5
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_contact2999SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.75 Å / Total num. of bins used: 36
RfactorNum. reflection% reflection
Rfree0.3375 -6.25 %
Rwork0.2482 375 -
all0.2533 400 -
obs--98.27 %

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