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- PDB-6jeg: Crystal structure of calcium free human gelsolin amyloid mutant G167R -

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Basic information

Entry
Database: PDB / ID: 6jeg
TitleCrystal structure of calcium free human gelsolin amyloid mutant G167R
ComponentsGelsolin
KeywordsActin Binding Protein / gelsolin / amyloidosis / calcium activation
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 / sarcoplasm / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.975 Å
AuthorsZorgati, H. / Robinson, R.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The role of gelsolin domain 3 in familial amyloidosis (Finnish type).
Authors: Zorgati, H. / Larsson, M. / Ren, W. / Sim, A.Y.L. / Gettemans, J. / Grimes, J.M. / Li, W. / Robinson, R.C.
History
DepositionFeb 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Gelsolin
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,3954
Polymers161,2112
Non-polymers1842
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-3 kcal/mol
Surface area62430 Å2
Unit cell
Length a, b, c (Å)172.274, 172.274, 150.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 80605.266 Da / Num. of mol.: 2 / Mutation: G167R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 15% glycerol, 1.5M ammonium sulfate, 0.1M tris HCl, pH8.5

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.97→19.78 Å / Num. obs: 45030 / % possible obs: 96.4 % / Redundancy: 11.2 % / Net I/σ(I): 10
Reflection shellResolution: 2.97→3.08 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFN

3ffn


Resolution: 2.975→19.78 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.61
RfactorNum. reflection% reflection
Rfree0.2372 2333 5.18 %
Rwork0.1981 --
obs0.2001 45030 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.975→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11188 0 12 3 11203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511452
X-RAY DIFFRACTIONf_angle_d0.95515509
X-RAY DIFFRACTIONf_dihedral_angle_d23.5794205
X-RAY DIFFRACTIONf_chiral_restr0.0541651
X-RAY DIFFRACTIONf_plane_restr0.0052048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9747-3.03520.2777880.26181412X-RAY DIFFRACTION56
3.0352-3.1010.32911360.26372202X-RAY DIFFRACTION87
3.101-3.17280.29011400.2772534X-RAY DIFFRACTION98
3.1728-3.25180.33331210.25562568X-RAY DIFFRACTION100
3.2518-3.33930.29511550.23852548X-RAY DIFFRACTION100
3.3393-3.43710.26711450.23122564X-RAY DIFFRACTION100
3.4371-3.54740.30011320.22982571X-RAY DIFFRACTION100
3.5474-3.67350.26491240.21862605X-RAY DIFFRACTION100
3.6735-3.81950.21411140.20132618X-RAY DIFFRACTION100
3.8195-3.9920.2441540.18892554X-RAY DIFFRACTION100
3.992-4.20060.24221460.18532610X-RAY DIFFRACTION100
4.2006-4.46090.20011300.15722591X-RAY DIFFRACTION100
4.4609-4.80080.20171570.16362601X-RAY DIFFRACTION100
4.8008-5.27560.22011460.17722617X-RAY DIFFRACTION100
5.2756-6.02010.24481490.19592643X-RAY DIFFRACTION100
6.0201-7.51490.22481410.20162691X-RAY DIFFRACTION100
7.5149-19.78070.17261550.16882768X-RAY DIFFRACTION99
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)
11.072-0.04290.65881.94120.67734.3753-0.2391-0.09670.0010.23590.21210.2973-0.3365-0.20020.03250.63160.2681-0.00920.3467-0.00020.392744.8973-16.765552.0697
20.4723-0.74720.05712.83050.09181.40850.09040.4272-0.2062-0.4972-0.1145-0.10990.27880.32250.02470.53910.12640.00140.4326-0.01190.401749.9886-8.07232.3647
31.84440.9171-0.26785.0312-1.11912.1786-0.11420.2032-0.0417-0.65010.07970.21050.26140.11360.01580.31840.0992-0.13510.2921-0.08290.27439.282918.567130.2491
42.0152-0.0191-0.98461.19090.80013.8680.2773-0.0839-0.18950.3398-0.2287-0.2172-0.25960.103-0.07640.5519-0.2167-0.02320.3004-0.02010.392735.271956.913560.2239
51.3090.78391.26520.58691.03543.57840.4312-0.19930.06080.123-0.30330.14820.0139-0.2273-0.15210.5579-0.05360.1430.27510.01010.486622.988258.406460.1907
63.53810.2002-0.90350.9703-0.29961.1676-0.03690.387-0.7668-0.0137-0.1111-0.01430.0478-0.16520.12410.29790.0686-0.04460.2535-0.12830.38146.298436.851545.64
75.34090.46640.09772.0722-0.1742.3030.06510.931-0.3232-0.2803-0.14870.11280.0445-0.29080.09120.22890.07970.01990.4128-0.120.41755.091937.151442.5671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 410 )
3X-RAY DIFFRACTION3chain 'A' and (resid 411 through 755 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 182 )
5X-RAY DIFFRACTION5chain 'B' and (resid 183 through 341 )
6X-RAY DIFFRACTION6chain 'B' and (resid 342 through 489 )
7X-RAY DIFFRACTION7chain 'B' and (resid 490 through 755 )

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