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- PDB-9r74: Pyrin B30.2 domain, FMF mutation I641F -

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Basic information

Entry
Database: PDB / ID: 9r74
TitlePyrin B30.2 domain, FMF mutation I641F
ComponentsPyrin
KeywordsSIGNALING PROTEIN / Familial Mediterranean fever / MEFV
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 / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production / pyroptotic inflammatory response ...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 / pattern recognition receptor signaling pathway / microtubule associated complex / negative regulation of interleukin-1 beta production / pyroptotic inflammatory response / The NLRP3 inflammasome / response to type II interferon / Purinergic signaling in leishmaniasis infection / ruffle / negative regulation of cytokine production involved in inflammatory response / positive regulation of autophagy / autophagosome / positive regulation of interleukin-1 beta production / negative regulation of inflammatory response / positive regulation of inflammatory response / ubiquitin protein ligase activity / lamellipodium / actin binding / regulation of gene expression / cytoplasmic vesicle / microtubule / inflammatory response / innate immune response / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger ...DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / : / SPRY-associated domain / SPRY-associated / PRY / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Death-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / THIOCYANATE ION / Pyrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsMittl, P. / Possner, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Pyrin B30.2 domain, FMF mutation I641F
Authors: Mittl, P. / Possner, D.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3355
Polymers21,0981
Non-polymers2374
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-1 kcal/mol
Surface area9530 Å2
Unit cell
Length a, b, c (Å)60.127, 60.127, 180.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

21A-1025-

HOH

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Components

#1: Protein Pyrin / Marenostrin


Mass: 21098.094 Da / Num. of mol.: 1 / Mutation: I641F
Source method: isolated from a genetically manipulated source
Details: Pyrin B30.2 domain with FMF mutation I641F / Source: (gene. exp.) Homo sapiens (human) / Gene: MEFV, MEF, TRIM20 / Production host: Escherichia coli (E. coli) / References: UniProt: O15553
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-AcOH, pH 7.6; 0.2 M KSCN; 20 % (w/v) PEG 2k MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→45.12 Å / Num. obs: 13775 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.981 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.133 / Rrim(I) all: 0.26 / Χ2: 0.92 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 3.3 % / Rmerge(I) obs: 1.141 / Num. measured all: 3222 / Num. unique obs: 970 / CC1/2: 0.355 / Rpim(I) all: 0.71 / Rrim(I) all: 1.351 / Χ2: 0.92 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→45.1 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.882 / SU B: 15.075 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27644 703 5.1 %RANDOM
Rwork0.20739 ---
obs0.21101 13018 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.33 Å2-0 Å2
2---0.67 Å20 Å2
3---2.17 Å2
Refinement stepCycle: 1 / Resolution: 2→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 14 127 1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121553
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161455
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.7972116
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7373358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4115200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.5511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9910245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6561.438776
X-RAY DIFFRACTIONr_mcbond_other1.5361.425772
X-RAY DIFFRACTIONr_mcangle_it2.7482.554967
X-RAY DIFFRACTIONr_mcangle_other2.7512.558968
X-RAY DIFFRACTIONr_scbond_it1.5681.613777
X-RAY DIFFRACTIONr_scbond_other1.4671.609777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5592.8641144
X-RAY DIFFRACTIONr_long_range_B_refined5.77415.921783
X-RAY DIFFRACTIONr_long_range_B_other5.7314.611756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 49 -
Rwork0.321 920 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.2636 Å / Origin y: -22.046 Å / Origin z: 6.4814 Å
111213212223313233
T0.0187 Å2-0.0199 Å2-0.0003 Å2-0.041 Å2-0.0209 Å2--0.0381 Å2
L3.3912 °2-0.7117 °2-0.0126 °2-2.4756 °21.0119 °2--2.7634 °2
S0.0431 Å °0.0523 Å °-0.31 Å °0.0853 Å °-0.0088 Å °-0.0177 Å °0.1716 Å °-0.0777 Å °-0.0343 Å °

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