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- PDB-7e5b: Crystal structure of ASC PYD Domain and Rb-B7 -

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Basic information

Entry
Database: PDB / ID: 7e5b
TitleCrystal structure of ASC PYD Domain and Rb-B7
Components
  • Apoptosis-associated speck-like protein containing a CARD
  • Repebody (Rb-B7)
KeywordsPROTEIN BINDING / Inflammasome / Apoptosis
Function / homology
Function and homology information


Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / macropinocytosis ...Pyrin domain binding / NLRP6 inflammasome complex / myosin I binding / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / myeloid dendritic cell activation involved in immune response / regulation of intrinsic apoptotic signaling pathway / myeloid dendritic cell activation / IkappaB kinase complex / The AIM2 inflammasome / macropinocytosis / AIM2 inflammasome complex / icosanoid biosynthetic process / interleukin-6 receptor binding / NLRP1 inflammasome complex / canonical inflammasome complex / NLRP3 inflammasome complex assembly / positive regulation of adaptive immune response / BMP receptor binding / NLRP3 inflammasome complex / negative regulation of protein serine/threonine kinase activity / negative regulation of interferon-beta production / CLEC7A/inflammasome pathway / positive regulation of cysteine-type endopeptidase activity / regulation of tumor necrosis factor-mediated signaling pathway / osmosensory signaling pathway / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage cytokine production / pattern recognition receptor signaling pathway / positive regulation of actin filament polymerization / negative regulation of NF-kappaB transcription factor activity / tropomyosin binding / positive regulation of activated T cell proliferation / pyroptotic inflammatory response / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / The NLRP3 inflammasome / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cytokine production involved in inflammatory response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of T cell migration / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / negative regulation of canonical NF-kappaB signal transduction / positive regulation of phagocytosis / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein stability / protein homooligomerization / positive regulation of DNA-binding transcription factor activity / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / azurophil granule lumen / positive regulation of type II interferon production / positive regulation of T cell activation / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / secretory granule lumen / defense response to Gram-negative bacterium / microtubule / defense response to virus / protease binding / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / protein dimerization activity / defense response to Gram-positive bacterium / positive regulation of apoptotic process / Golgi membrane / innate immune response / neuronal cell body / apoptotic process / Neutrophil degranulation / nucleolus / enzyme binding / endoplasmic reticulum / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
CARD8/ASC/NALP1, CARD domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Apoptosis-associated speck-like protein containing a CARD
Similarity search - Component
Biological speciesCyclostomata (jawless vertebrates)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsCho, H.S. / Cha, J.S.
CitationJournal: Cell Death Discov / Year: 2023
Title: Oligomeric states of ASC specks regulate inflammatory responses by inflammasome in the extracellular space.
Authors: Yu, T.G. / Cha, J.S. / Kim, G. / Sohn, Y.K. / Yoo, Y. / Kim, U. / Song, J.J. / Cho, H.S. / Kim, H.S.
History
DepositionFeb 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Repebody (Rb-B7)
B: Repebody (Rb-B7)
C: Apoptosis-associated speck-like protein containing a CARD
D: Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3306
Polymers80,1464
Non-polymers1842
Water2,774154
1
A: Repebody (Rb-B7)
D: Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1653
Polymers40,0732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-5 kcal/mol
Surface area14690 Å2
MethodPISA
2
B: Repebody (Rb-B7)
C: Apoptosis-associated speck-like protein containing a CARD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1653
Polymers40,0732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-2 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.481, 79.481, 279.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Repebody (Rb-B7)


Mass: 29852.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyclostomata (jawless vertebrates) / Production host: Escherichia coli (E. coli)
#2: Protein Apoptosis-associated speck-like protein containing a CARD / hASC / Caspase recruitment domain-containing protein 5 / PYD and CARD domain-containing protein / ...hASC / Caspase recruitment domain-containing protein 5 / PYD and CARD domain-containing protein / Target of methylation-induced silencing 1


Mass: 10220.779 Da / Num. of mol.: 2 / Fragment: PYD Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PYCARD, ASC, CARD5, TMS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULZ3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris:HCl pH 5.5, 25% (w/v) PEG 3350, 0.1M TCEP hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.29→29.65 Å / Num. obs: 40516 / % possible obs: 98.19 % / Redundancy: 15.8 % / Biso Wilson estimate: 39.71 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.9
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3978 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBX

6lbx


Resolution: 2.29→29.65 Å / SU ML: 0.2866 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 21.4812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 2000 4.94 %
Rwork0.1951 38516 -
obs0.1972 40516 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.45 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5381 0 12 154 5547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085480
X-RAY DIFFRACTIONf_angle_d0.97417470
X-RAY DIFFRACTIONf_chiral_restr0.0511905
X-RAY DIFFRACTIONf_plane_restr0.0057966
X-RAY DIFFRACTIONf_dihedral_angle_d19.97671962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.350.30761400.28062708X-RAY DIFFRACTION98.68
2.35-2.410.32961430.26512739X-RAY DIFFRACTION99.86
2.41-2.490.32031410.25442733X-RAY DIFFRACTION99.9
2.49-2.570.27121440.23972758X-RAY DIFFRACTION99.9
2.57-2.660.28961420.22242737X-RAY DIFFRACTION100
2.66-2.760.26141430.21892755X-RAY DIFFRACTION99.97
2.76-2.890.28931430.22952759X-RAY DIFFRACTION99.97
2.89-3.040.30061450.23522772X-RAY DIFFRACTION99.93
3.04-3.230.29241430.22422778X-RAY DIFFRACTION99.93
3.23-3.480.23061450.21432798X-RAY DIFFRACTION100
3.48-3.830.24121240.19882360X-RAY DIFFRACTION84.12
3.83-4.380.17861380.1532680X-RAY DIFFRACTION94.34
4.38-5.520.19891500.15712884X-RAY DIFFRACTION99.74
5.52-29.650.19011590.15783055X-RAY DIFFRACTION99.6
Refinement TLS params.Method: refined / Origin x: 7.2288 Å / Origin y: -0.5061 Å / Origin z: 31.1913 Å
111213212223313233
T0.5509 Å2-0.002 Å20.056 Å2-0.2124 Å2-0.0063 Å2--0.3349 Å2
L0.8968 °2-0.3904 °20.4901 °2-0.4797 °2-0.3438 °2--0.6187 °2
S-0.223 Å °-0.1025 Å °0.0206 Å °0.2483 Å °0.1672 Å °0.0233 Å °-0.1272 Å °-0.0621 Å °0.0567 Å °
Refinement TLS groupSelection details: all

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