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- PDB-5faf: N184K pathological variant of gelsolin domain 2 (orthorhombic form) -

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Basic information

Entry
Database: PDB / ID: 5faf
TitleN184K pathological variant of gelsolin domain 2 (orthorhombic form)
ComponentsGelsolin
KeywordsSTRUCTURAL PROTEIN / amyloidosis / calcium / mutation / actin
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 / 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / 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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / cilium assembly / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / blood microparticle / secretory granule lumen / 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
ACETATE ION / Gelsolin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6689
Polymers13,1821
Non-polymers4868
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-32 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.390, 50.120, 80.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-302-

GOL

21A-302-

GOL

31A-303-

CA

41A-455-

HOH

51A-472-

HOH

61A-518-

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, 198 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG 8000 0.1 M MES 0.2 M calcium acetate

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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
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.05→42.5 Å / Num. obs: 48782 / % possible obs: 96.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.3
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.4 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KCQ

1kcq


Resolution: 1.05→42.5 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.984 / SU B: 1.566 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16816 2000 4.1 %RANDOM
Rwork0.13049 ---
obs0.13204 46744 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.028 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.9 Å20 Å2
3---1.65 Å2
Refinement stepCycle: 1 / Resolution: 1.05→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms884 0 26 190 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191053
X-RAY DIFFRACTIONr_bond_other_d0.0010.021022
X-RAY DIFFRACTIONr_angle_refined_deg2.1671.9571446
X-RAY DIFFRACTIONr_angle_other_deg2.67132376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5635149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45223.44858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22515196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0461514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211243
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02259
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_it3.7771.578492
X-RAY DIFFRACTIONr_mcbond_other3.3891.559490
X-RAY DIFFRACTIONr_mcangle_it4.0342.353622
X-RAY DIFFRACTIONr_mcangle_other4.0412.357623
X-RAY DIFFRACTIONr_scbond_it8.4312.137560
X-RAY DIFFRACTIONr_scbond_other8.4242.143561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2143.037804
X-RAY DIFFRACTIONr_long_range_B_refined13.03718.351383
X-RAY DIFFRACTIONr_long_range_B_other10.28415.9911262
X-RAY DIFFRACTIONr_rigid_bond_restr20.23832074
X-RAY DIFFRACTIONr_sphericity_free44.242534
X-RAY DIFFRACTIONr_sphericity_bonded23.07852203
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 128 -
Rwork0.411 3007 -
obs--85.54 %

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