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- PDB-4cg4: Crystal structure of the CHS-B30.2 domains of TRIM20 -

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Basic information

Entry
Database: PDB / ID: 4cg4
TitleCrystal structure of the CHS-B30.2 domains of TRIM20
ComponentsPYRIN
KeywordsACTIN-BINDING PROTEIN / FAMILIAL MEDITERRANEAN FEVER
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 domain / 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 ...SPRY domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-AMINO-ETHANETHIOL / Pyrin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWeinert, C. / Morger, D. / Djekic, A. / Mittl, P.R.E. / Gruetter, M.G.
CitationJournal: Sci.Rep. / Year: 2015
Title: Crystal Structure of Trim20 C-Terminal Coiled-Coil/B30.2 Fragment: Implications for the Recognition of Higher Order Oligomers
Authors: Weinert, C. / Morger, D. / Djekic, A. / Mittl, P.R.E. / Gruetter, M.G.
History
DepositionNov 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status / struct_conn
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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: PYRIN
F: PYRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,91521
Polymers256,6376
Non-polymers1,27815
Water59433
1
A: PYRIN
B: PYRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8005
Polymers85,5462
Non-polymers2543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-103 kcal/mol
Surface area40610 Å2
MethodPISA
2
C: PYRIN
D: PYRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0318
Polymers85,5462
Non-polymers4866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-130.4 kcal/mol
Surface area41640 Å2
MethodPISA
3
E: PYRIN
F: PYRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0848
Polymers85,5462
Non-polymers5396
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-105.4 kcal/mol
Surface area41850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.820, 388.210, 70.880
Angle α, β, γ (deg.)90.00, 116.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PYRIN / TRIM20 / MARENOSTRIN


Mass: 42772.766 Da / Num. of mol.: 6 / Fragment: CHS-B30.2, RESIDUES 413-781
Source method: isolated from a genetically manipulated source
Details: DISULPHIDE BOND BETWEEN CYSTEAMINE AND CYSTEINE FOR DHL C1 AND CYS C639 DHL C2 AND CYS C773 DHL D3 AND CYS D639 DHL E4 AND CYS E639 DHL F5 AND CYS F639
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFX3CH / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O15553
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H7NS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-AMINO-ETHANETHIOL (DHL): COVALENTLY ATTACHED TO CYSTEINS

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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: 3.35 Å3/Da / Density % sol: 63.33 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M TRIS-ACOH PH 7.4-8, 0.26% (W/V) CYSTAMINE-HCL, 0.2 M LISO4, 8% (W/V) PEG 20000, 8% (W/V) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2011 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.53 Å / Num. obs: 129351 / % possible obs: 98.9 % / Observed criterion σ(I): 0.88 / Redundancy: 7.4 % / Biso Wilson estimate: 45.41 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.77
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.88 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WL1

2wl1


Resolution: 2.4→48.526 Å / SU ML: 0.42 / σ(F): 1.36 / Phase error: 32.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 6466 5 %
Rwork0.2115 --
obs0.214 129351 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 5.8014 Å2 / ksol: 1.3743 e/Å3
Displacement parametersBiso mean: 54.8 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17943 0 68 33 18044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01218388
X-RAY DIFFRACTIONf_angle_d1.37824834
X-RAY DIFFRACTIONf_dihedral_angle_d12.9896977
X-RAY DIFFRACTIONf_chiral_restr0.0592701
X-RAY DIFFRACTIONf_plane_restr0.0073200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.40912060.36793503X-RAY DIFFRACTION86
2.4273-2.45590.34782270.33853943X-RAY DIFFRACTION95
2.4559-2.48580.33931990.32124043X-RAY DIFFRACTION98
2.4858-2.51730.39822180.3094070X-RAY DIFFRACTION99
2.5173-2.55040.35562010.31054152X-RAY DIFFRACTION99
2.5504-2.58530.35492260.29974075X-RAY DIFFRACTION99
2.5853-2.62230.37742570.29764063X-RAY DIFFRACTION99
2.6223-2.66140.34852150.29274091X-RAY DIFFRACTION99
2.6614-2.7030.33422040.28184120X-RAY DIFFRACTION99
2.703-2.74730.3591830.28844134X-RAY DIFFRACTION100
2.7473-2.79470.36472200.29254126X-RAY DIFFRACTION99
2.7947-2.84550.36881870.29384187X-RAY DIFFRACTION100
2.8455-2.90020.32842030.27774083X-RAY DIFFRACTION99
2.9002-2.95940.34132070.27364164X-RAY DIFFRACTION99
2.9594-3.02370.34552210.26524059X-RAY DIFFRACTION99
3.0237-3.0940.35872070.26284175X-RAY DIFFRACTION100
3.094-3.17140.33262250.25894109X-RAY DIFFRACTION100
3.1714-3.25710.29382220.25184102X-RAY DIFFRACTION100
3.2571-3.3530.32062300.24394153X-RAY DIFFRACTION100
3.353-3.46120.30662190.22354094X-RAY DIFFRACTION100
3.4612-3.58480.23742100.20764130X-RAY DIFFRACTION100
3.5848-3.72830.26592430.20074167X-RAY DIFFRACTION100
3.7283-3.89790.23182260.19334110X-RAY DIFFRACTION100
3.8979-4.10330.22972270.17964132X-RAY DIFFRACTION100
4.1033-4.36030.2142120.16244146X-RAY DIFFRACTION100
4.3603-4.69670.18481940.14894157X-RAY DIFFRACTION100
4.6967-5.16880.18512310.14284090X-RAY DIFFRACTION100
5.1688-5.91560.22712140.18084196X-RAY DIFFRACTION100
5.9156-7.44870.19892120.18284155X-RAY DIFFRACTION100
7.4487-48.53610.17312200.1484156X-RAY DIFFRACTION100

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