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- PDB-8sdj: Hydrophobic Interactions Drive the Tetrameric Assembly of the TRI... -

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Basic information

Entry
Database: PDB / ID: 8sdj
TitleHydrophobic Interactions Drive the Tetrameric Assembly of the TRIM20 Coiled-Coil Domain
ComponentsPyrin
KeywordsLIGASE / E3 ubiquitin ligase / Ubiquitination / coiled-coil
Function / homology
Function and homology information


pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / canonical inflammasome complex / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production ...pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / canonical inflammasome complex / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production / pyroptotic inflammatory response / response to type II interferon / The NLRP3 inflammasome / negative regulation of cytokine production involved in inflammatory response / autophagosome / positive regulation of autophagy / Purinergic signaling in leishmaniasis infection / ruffle / positive regulation of interleukin-1 beta production / negative regulation of inflammatory response / positive regulation of inflammatory response / ubiquitin protein ligase activity / lamellipodium / actin binding / cytoplasmic vesicle / regulation of gene expression / microtubule / protein ubiquitination / inflammatory response / innate immune response / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
SPRY-associated domain / SPRY-associated / PRY / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger ...SPRY-associated domain / SPRY-associated / PRY / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Death-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLou, X.H. / Ma, B.B. / Zhuang, Y. / Li, X.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI155488 United States
CitationJournal: To Be Published
Title: Hydrophobic Interactions Drive the Tetrameric Assembly of the TRIM20 Coiled-Coil Domain
Authors: Lou, X.H. / Ma, B.B. / Zhuang, Y. / Li, X.C.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrin
B: Pyrin
C: Pyrin
D: Pyrin


Theoretical massNumber of molelcules
Total (without water)51,7034
Polymers51,7034
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS was used to determine the tetrameric state.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16560 Å2
ΔGint-135 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.600, 38.830, 164.300
Angle α, β, γ (deg.)90.000, 89.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyrin / Marenostrin


Mass: 12925.697 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEFV, MEF, TRIM20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15553

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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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: 0.1M HEPES pH8.0, 35% 1,2-Propanediol, 10% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→9 Å / Num. obs: 18553 / % possible obs: 95.7 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 4 / Num. unique obs: 2593 / CC1/2: 0.991 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.737 / ESU R Free: 0.334 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.294 838 4.518 %
Rwork0.259 17710 -
all0.261 --
obs-18548 95.094 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 75.81 Å2
Baniso -1Baniso -2Baniso -3
1-5.141 Å20 Å20.154 Å2
2--5.94 Å2-0 Å2
3----11.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 0 0 3636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123779
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.6385055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5423.778225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.70315798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4391524
X-RAY DIFFRACTIONr_chiral_restr0.1350.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022824
X-RAY DIFFRACTIONr_nbd_refined0.2550.21685
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2129
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2930.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.27
X-RAY DIFFRACTIONr_mcbond_it7.7636.9831826
X-RAY DIFFRACTIONr_mcangle_it10.72710.4342287
X-RAY DIFFRACTIONr_scbond_it10.677.9551953
X-RAY DIFFRACTIONr_scangle_it15.1211.5462759
X-RAY DIFFRACTIONr_lrange_it16.773131.5214850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.4-2.4580.569380.41912130.42312970.5460.64396.45340.401
2.458-2.520.735490.36811190.37912770.5540.66691.46440.346
2.52-2.5870.462440.38712390.3913270.5350.66296.68420.379
2.587-2.660.513360.34311130.34811680.6770.73498.37330.326
2.66-2.7390.577240.31511990.32212420.7450.79998.47020.3
2.739-2.8260.285310.24510760.24611210.8940.85798.75110.233
2.826-2.9210.379470.2710700.27311360.6920.83298.32750.266
2.921-3.0270.353680.27810130.28310990.8020.82398.36210.271
3.027-3.1460.415570.2779680.28510390.9130.85998.65250.265
3.146-3.280.345560.2439320.24810120.8470.90597.62850.229
3.28-3.4320.394620.2388880.2489880.9130.92196.15380.231
3.432-3.6070.271440.2398130.249200.9070.92593.15220.238
3.607-3.8130.238350.2477930.2478780.9260.91794.30520.253
3.813-4.0580.247490.2277470.2288070.9440.9398.63690.234
4.058-4.3580.148420.2027780.1988230.9770.95199.63550.215
4.358-4.7350.179530.2286500.2237060.9490.93299.57510.26
4.735-5.2320.347270.2086280.2136590.8640.93499.3930.243
5.232-5.9260.356130.2695900.2716120.870.89498.52940.288
5.926-70.62390.2994760.3165330.7570.92696.62290.343
7-90.186240.34050.2944410.9440.96497.27890.371

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