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- PDB-4ikm: X-ray structure of CARD8 CARD domain -

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Basic information

Entry
Database: PDB / ID: 4ikm
TitleX-ray structure of CARD8 CARD domain
ComponentsMaltose-binding periplasmic protein, Caspase recruitment domain-containing protein 8
KeywordsSIGNALING PROTEIN / Death fold superfamily / six-helix bundle / inflammasome / apoptosis / innate immune system / signal transduction
Function / homology
Function and homology information


CARD8 inflammasome complex assembly / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / negative regulation of lipopolysaccharide-mediated signaling pathway / self proteolysis ...CARD8 inflammasome complex assembly / NACHT domain binding / Formation of apoptosome / cysteine-type endopeptidase activator activity / inhibition of cysteine-type endopeptidase activity / negative regulation of NLRP3 inflammasome complex assembly / NLRP3 inflammasome complex / CARD domain binding / negative regulation of lipopolysaccharide-mediated signaling pathway / self proteolysis / Regulation of the apoptosome activity / Hydrolases; Acting on peptide bonds (peptidases) / regulation of canonical NF-kappaB signal transduction / pattern recognition receptor activity / negative regulation of interleukin-1 beta production / detection of maltose stimulus / maltose binding / negative regulation of NF-kappaB transcription factor activity / maltose transport complex / maltose transport / maltodextrin transmembrane transport / antiviral innate immune response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / molecular condensate scaffold activity / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of interleukin-1 beta production / outer membrane-bounded periplasmic space / peptidase activity / defense response to virus / regulation of apoptotic process / periplasmic space / DNA damage response / protein homodimerization activity / protein-containing complex / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
FIIND domain / Function to find / FIIND domain profile. / Death Domain, Fas / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site ...FIIND domain / Function to find / FIIND domain profile. / Death Domain, Fas / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / IODIDE ION / Maltose/maltodextrin-binding periplasmic protein / Caspase recruitment domain-containing protein 8
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4606 Å
AuthorsJin, T. / Huang, M. / Smith, P. / Jiang, J. / Xiao, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The structure of the CARD8 caspase-recruitment domain suggests its association with the FIIND domain and procaspases through adjacent surfaces.
Authors: Jin, T. / Huang, M. / Smith, P. / Jiang, J. / Xiao, T.S.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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
A: Maltose-binding periplasmic protein, Caspase recruitment domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0886
Polymers53,3681
Non-polymers7205
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.877, 94.877, 219.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Maltose-binding periplasmic protein, Caspase recruitment domain-containing protein 8 / MBP / MMBP / Maltodextrin-binding protein / Apoptotic protein NDPP1 / CARD-inhibitor of NF-kappa-B- ...MBP / MMBP / Maltodextrin-binding protein / Apoptotic protein NDPP1 / CARD-inhibitor of NF-kappa-B-activating ligand / CARDINAL / DACAR / Tumor up-regulated CARD-containing antagonist of CASP9 / TUCAN


Mass: 53368.055 Da / Num. of mol.: 1 / Fragment: MBP tagged human CARD8 CARD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Strain: K12
Gene: b4034, CARD8, TUCAN, CARDINAL, JW3994, malE, KIAA0955, NDPP1
Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: Q9Y2G2
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 16% PEG8000, 0.1 M NaI, 0.1 M NaAc, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 21995 / Num. obs: 21951 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 3.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1217)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VD8

3vd8


Resolution: 2.4606→47.438 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1121 5.12 %
Rwork0.2007 --
obs0.2032 21881 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4606→47.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3601 0 33 69 3703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043706
X-RAY DIFFRACTIONf_angle_d0.8535033
X-RAY DIFFRACTIONf_dihedral_angle_d11.5861343
X-RAY DIFFRACTIONf_chiral_restr0.057558
X-RAY DIFFRACTIONf_plane_restr0.004649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4606-2.57260.371440.28592443X-RAY DIFFRACTION96
2.5726-2.70820.33791410.26062543X-RAY DIFFRACTION100
2.7082-2.87790.29721410.24172548X-RAY DIFFRACTION100
2.8779-3.10010.28551400.24032555X-RAY DIFFRACTION100
3.1001-3.4120.27061420.21622582X-RAY DIFFRACTION100
3.412-3.90550.28091380.18862614X-RAY DIFFRACTION100
3.9055-4.91970.19911440.16762648X-RAY DIFFRACTION100
4.9197-47.44730.24081310.19822827X-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)
12.8538-4.08791.48029.78680.0745.5406-0.1107-0.0562-1.175-0.80140.489-0.42470.7249-0.21-0.29910.557-0.13940.27360.62950.03020.92533.3915-54.1861-0.7869
23.2509-0.898-0.21515.39410.11232.8044-0.21670.609-0.0013-0.71460.3009-0.0615-0.1726-0.2153-0.08130.5223-0.1290.15080.60590.14090.5155-0.6181-32.6164-3.8111
33.4275-1.99991.27635.97740.68293.9627-0.61220.1362-0.0490.26320.32050.55430.3059-0.47210.28120.4260.00380.09430.5770.17150.6639-3.3901-27.01863.0953
43.2551-0.11341.5755.4574-5.60116.96990.338-0.24550.87550.5682-0.31-0.4824-0.6356-0.24890.02650.78370.14770.21240.61480.07160.8813-5.4126-30.795728.1006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 315 )
3X-RAY DIFFRACTION3chain 'A' and (resid 316 through 357 )
4X-RAY DIFFRACTION4chain 'A' and (resid 358 through 463 )

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