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- PDB-9r70: Pyrin B30.2 domain, FMF mutation M680L -

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Basic information

Entry
Database: PDB / ID: 9r70
TitlePyrin B30.2 domain, FMF mutation M680L
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 / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / microtubule associated complex / negative regulation of interleukin-1 beta production / pattern recognition receptor signaling pathway / The NLRP3 inflammasome / pyroptotic inflammatory response ...pyroptosome complex assembly / negative regulation of macrophage inflammatory protein 1 alpha production / regulation of interleukin-1 beta production / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-12 production / microtubule associated complex / negative regulation of interleukin-1 beta production / pattern recognition receptor signaling pathway / The NLRP3 inflammasome / pyroptotic inflammatory response / Purinergic signaling in leishmaniasis infection / ruffle / negative regulation of cytokine production involved in inflammatory response / response to type II interferon / positive regulation of autophagy / autophagosome / positive regulation of interleukin-1 beta production / negative regulation of inflammatory response / regulation of gene expression / ubiquitin protein ligase activity / lamellipodium / actin binding / cytoplasmic vesicle / microtubule / inflammatory response / innate immune response / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / : / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain ...DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / : / SPRY-associated domain / SPRY-associated / PRY / B-box zinc finger / Butyrophylin-like, SPRY domain / 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
THIOCYANATE ION / Pyrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMittl, P. / Possner, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
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. / Grutter, M.G. / Mittl, P.R.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7053
Polymers21,5851
Non-polymers1202
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint3 kcal/mol
Surface area9400 Å2
Unit cell
Length a, b, c (Å)42.364, 60.231, 84.051
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: 21584.723 Da / Num. of mol.: 1 / Mutation: M680L
Source method: isolated from a genetically manipulated source
Details: FMF mutation M680L / Source: (gene. exp.) Homo sapiens (human) / Gene: MEFV, MEF, TRIM20 / Production host: Escherichia coli (E. coli) / References: UniProt: O15553
#2: Chemical ChemComp-SCN / THIOCYANATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-AcOH, pH 8.0; 0.2 M KSCN; 23.3 % (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 PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→48.96 Å / Num. obs: 32908 / % possible obs: 93.6 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.032 / Rrim(I) all: 0.106 / Χ2: 0.98 / Net I/σ(I): 14.2 / Num. measured all: 335757
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 56.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 1.439 / Num. measured all: 3835 / Num. unique obs: 937 / CC1/2: 0.949 / Rpim(I) all: 0.818 / Rrim(I) all: 1.666 / Χ2: 1.08 / Net I/σ(I) obs: 0.9

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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: 1.5→48.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.163 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21205 1621 5 %RANDOM
Rwork0.17774 ---
obs0.1794 31079 92.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.324 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0 Å2
2---0.57 Å20 Å2
3---0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.5→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 7 212 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121633
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161538
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.8052230
X-RAY DIFFRACTIONr_angle_other_deg0.6271.7433557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1815212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.549513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68510267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
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_it1.5151.172816
X-RAY DIFFRACTIONr_mcbond_other1.4551.162814
X-RAY DIFFRACTIONr_mcangle_it2.4012.0881029
X-RAY DIFFRACTIONr_mcangle_other2.4012.0941030
X-RAY DIFFRACTIONr_scbond_it2.2851.404817
X-RAY DIFFRACTIONr_scbond_other2.2841.407818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5322.4491199
X-RAY DIFFRACTIONr_long_range_B_refined7.18818.111915
X-RAY DIFFRACTIONr_long_range_B_other6.87113.081830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 70 -
Rwork0.401 1383 -
obs--57.2 %
Refinement TLS params.Method: refined / Origin x: 6.2865 Å / Origin y: -7.5863 Å / Origin z: -15.953 Å
111213212223313233
T0.0766 Å20.0038 Å2-0.0146 Å2-0.0071 Å20.001 Å2--0.0052 Å2
L1.417 °2-0.1186 °20.2972 °2-2.5221 °2-0.6033 °2--1.8468 °2
S0.0379 Å °0.0644 Å °0.0017 Å °-0.0408 Å °-0.0531 Å °-0.0687 Å °0.0132 Å °0.0979 Å °0.0152 Å °

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