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- PDB-9r6y: Pyrin B30.2 domain, FMF mutation R653H -

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Basic information

Entry
Database: PDB / ID: 9r6y
TitlePyrin B30.2 domain, FMF mutation R653H
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 / microtubule associated complex / pattern recognition receptor signaling pathway / 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 / microtubule associated complex / pattern recognition receptor signaling pathway / negative regulation of interleukin-1 beta production / pyroptotic inflammatory response / The NLRP3 inflammasome / response to type II interferon / Purinergic signaling in leishmaniasis infection / ruffle / positive regulation of autophagy / negative regulation of cytokine production involved in inflammatory response / 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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsMittl, P. / Possner, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Pyrin B30.2 domain, FMF mutation R653H
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)21,7515
Polymers21,5101
Non-polymers2414
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint6 kcal/mol
Surface area9340 Å2
Unit cell
Length a, b, c (Å)42.795, 60.595, 84.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyrin / Marenostrin


Mass: 21509.570 Da / Num. of mol.: 1 / Mutation: R653H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEFV, MEF, TRIM20 / Production host: Escherichia coli (E. coli) / References: UniProt: O15553
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na-Acetate, pH 5.5; 0.2 M KSCN; 25 % (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: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→42.79 Å / Num. obs: 53527 / % possible obs: 89.4 % / Redundancy: 44.4 % / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.015 / Rrim(I) all: 0.1 / Χ2: 0.83 / Net I/σ(I): 31.1 / Num. measured all: 2378289
Reflection shellResolution: 1.26→1.28 Å / % possible obs: 46.6 % / Redundancy: 19.8 % / Rmerge(I) obs: 1.547 / Num. measured all: 26612 / Num. unique obs: 1344 / CC1/2: 0.867 / Rpim(I) all: 0.337 / Rrim(I) all: 1.585 / Χ2: 0.41 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→42.08 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.255 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1567 2714 5.1 %RANDOM
Rwork0.13127 ---
obs0.13257 50675 89.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0 Å2
2---0.54 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.26→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 15 285 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121703
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161603
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.8042332
X-RAY DIFFRACTIONr_angle_other_deg0.6731.7423721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8065228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.45513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66910281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022072
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02400
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_it4.821.346852
X-RAY DIFFRACTIONr_mcbond_other4.711.339849
X-RAY DIFFRACTIONr_mcangle_it6.8012.4161082
X-RAY DIFFRACTIONr_mcangle_other6.8082.4191083
X-RAY DIFFRACTIONr_scbond_it6.7271.623851
X-RAY DIFFRACTIONr_scbond_other6.7251.625852
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4832.8261245
X-RAY DIFFRACTIONr_long_range_B_refined16.14417.871995
X-RAY DIFFRACTIONr_long_range_B_other14.31814.391897
X-RAY DIFFRACTIONr_rigid_bond_restr4.40933306
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.26→1.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 118 -
Rwork0.351 1997 -
obs--48.6 %

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