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- PDB-6jco: Crystal structure of calcium free human gelsolin amyloid mutant D187N -

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Basic information

Entry
Database: PDB / ID: 6jco
TitleCrystal structure of calcium free human gelsolin amyloid mutant D187N
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 / actin cap ...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 / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / podosome / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / actin filament organization / central nervous system development / protein destabilization / cellular response to type II interferon / actin filament binding / lamellipodium / actin cytoskeleton / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 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
DepositionJan 29, 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

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Assembly

Deposited unit
A: Gelsolin
B: Gelsolin


Theoretical massNumber of molelcules
Total (without water)160,5522
Polymers160,5522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-4 kcal/mol
Surface area61960 Å2
Unit cell
Length a, b, c (Å)170.130, 170.130, 151.480
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: 80275.898 Da / Num. of mol.: 2 / Mutation: D187N
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

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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: 3.45 Å3/Da / Density % sol: 64.39 %
Crystal growTemperature: 298.1 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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.88→69.193 Å / Num. obs: 50758 / % possible obs: 99.87 % / Redundancy: 12.6 % / Biso Wilson estimate: 71.85 Å2 / Net I/σ(I): 3.51
Reflection shellResolution: 2.88→2.98 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFN

3ffn


Resolution: 2.88→69.193 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 2500 4.93 %
Rwork0.2058 --
obs0.2088 50758 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→69.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11022 0 0 0 11022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111267
X-RAY DIFFRACTIONf_angle_d1.10915258
X-RAY DIFFRACTIONf_dihedral_angle_d4.9926685
X-RAY DIFFRACTIONf_chiral_restr0.0591627
X-RAY DIFFRACTIONf_plane_restr0.0072015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.93540.39051270.30882650X-RAY DIFFRACTION100
2.9354-2.99530.37661330.30072645X-RAY DIFFRACTION100
2.9953-3.06050.40371310.27512626X-RAY DIFFRACTION100
3.0605-3.13170.34411410.24942644X-RAY DIFFRACTION100
3.1317-3.210.31981500.24012636X-RAY DIFFRACTION100
3.21-3.29680.3331360.23762651X-RAY DIFFRACTION100
3.2968-3.39380.30541140.2392670X-RAY DIFFRACTION100
3.3938-3.50330.31941470.25212636X-RAY DIFFRACTION100
3.5033-3.62850.28671670.23232622X-RAY DIFFRACTION100
3.6285-3.77380.27411330.23332649X-RAY DIFFRACTION99
3.7738-3.94550.27851350.20442666X-RAY DIFFRACTION99
3.9455-4.15350.26831370.19262679X-RAY DIFFRACTION100
4.1535-4.41370.23561560.17692653X-RAY DIFFRACTION100
4.4137-4.75440.2421300.16032724X-RAY DIFFRACTION100
4.7544-5.23270.24781280.17532705X-RAY DIFFRACTION100
5.2327-5.98950.2871380.19452724X-RAY DIFFRACTION100
5.9895-7.54470.23811420.20292774X-RAY DIFFRACTION100
7.5447-69.21290.19551550.18622904X-RAY DIFFRACTION100

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