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- PDB-5fae: N184K pathological variant of gelsolin domain 2 (trigonal form) -

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Basic information

Entry
Database: PDB / ID: 5fae
TitleN184K pathological variant of gelsolin domain 2 (trigonal form)
ComponentsGelsolin
KeywordsSTRUCTURAL PROTEIN / gelsolin / amyloidosis / calcium / mutation
Function / homology
Function and homology information


striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / regulation of podosome assembly / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / : / positive regulation of actin nucleation ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / regulation of podosome assembly / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / : / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / podosome / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / actin filament organization / central nervous system development / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Gelsolin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBoni, F. / Milani, M. / Ricagno, S. / Bolognesi, M. / de Rosa, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
TelethonGEP15070 Italy
CitationJournal: Sci Rep / Year: 2016
Title: Molecular basis of a novel renal amyloidosis due to N184K gelsolin variant.
Authors: Boni, F. / Milani, M. / Porcari, R. / Barbiroli, A. / Ricagno, S. / de Rosa, M.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7488
Polymers13,1821
Non-polymers5667
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-53 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.919, 46.919, 84.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-476-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gelsolin / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 13181.726 Da / Num. of mol.: 1 / Fragment: UNP residues 178-293 / Mutation: N184K
Source method: isolated from a genetically manipulated source
Details: domain 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396

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Non-polymers , 5 types, 88 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M lithium sulfate 0.1 M tris 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.7→40.63 Å / Num. obs: 12405 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KCQ

1kcq


Resolution: 1.7→40.63 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 1236 9.99 %
Rwork0.1817 --
obs0.186 12367 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 29 81 948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019924
X-RAY DIFFRACTIONf_angle_d1.5381259
X-RAY DIFFRACTIONf_dihedral_angle_d14.971353
X-RAY DIFFRACTIONf_chiral_restr0.074135
X-RAY DIFFRACTIONf_plane_restr0.009166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7003-1.76840.30961360.26961216X-RAY DIFFRACTION100
1.7684-1.84890.30851360.23221202X-RAY DIFFRACTION99
1.8489-1.94630.26311390.2131214X-RAY DIFFRACTION100
1.9463-2.06830.22281330.19761212X-RAY DIFFRACTION100
2.0683-2.22790.23461340.18571226X-RAY DIFFRACTION100
2.2279-2.45210.25031350.18371232X-RAY DIFFRACTION100
2.4521-2.80690.2741370.18381232X-RAY DIFFRACTION100
2.8069-3.53610.23311390.17481263X-RAY DIFFRACTION100
3.5361-40.64470.17411470.16341334X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0230.578-0.10468.3096-1.37510.2175-0.38810.266-0.2898-1.32050.1325-1.35560.56860.06110.21410.76860.01530.12410.4641-0.06250.4133-13.9239-8.0092-5.5718
28.1465-4.25292.63476.5548-1.42756.99630.38361.04390.41-0.5371-0.38670.0391-0.11440.04040.03030.2082-0.02230.01390.2820.06480.1927-19.417422.1024-15.8548
35.5006-5.82580.37058.1783-0.38883.7791-0.22420.09740.62520.36620.0668-0.5263-0.39390.35280.18330.2211-0.0966-0.03690.2102-0.01540.2223-13.837323.7135-6.2147
44.0805-1.99191.11916.4961-1.29024.07770.0098-0.19070.21440.1008-0.03970.1266-0.069-0.16390.02090.1741-0.0332-0.00870.2051-0.0140.1642-22.489619.607-6.0911
54.1268-0.84461.52466.0065-2.52055.35020.0601-0.0419-0.2403-0.23160.0770.40150.368-0.3878-0.13620.1675-0.0337-0.01190.22780.02810.1856-29.012115.4079-11.9608
66.43122.12231.50773.71542.44254.680.6858-1.05360.3290.8687-0.5175-0.06880.16730.0485-0.1110.3712-0.08840.0190.2785-0.00130.2227-21.739218.52251.5677
74.94881.23881.01823.85134.18245.35290.1163-0.10180.55110.4448-0.65751.5314-0.1592-0.97710.5830.3867-0.0741-0.11510.3864-0.02920.4401-12.651729.53834.7159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 148 through 160 )
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 187 )
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 229 )
6X-RAY DIFFRACTION6chain 'A' and (resid 230 through 247 )
7X-RAY DIFFRACTION7chain 'A' and (resid 248 through 257 )

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