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- PDB-6jeh: Crystal structure of calcium free human gelsolin amyloid mutant D187Y -

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Basic information

Entry
Database: PDB / ID: 6jeh
TitleCrystal structure of calcium free human gelsolin amyloid mutant D187Y
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: 2.95 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


Theoretical massNumber of molelcules
Total (without water)160,6502
Polymers160,6502
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-1 kcal/mol
Surface area60570 Å2
Unit cell
Length a, b, c (Å)169.232, 169.232, 151.087
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: 80324.969 Da / Num. of mol.: 2 / Mutation: D187Y
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: 3.37 Å3/Da / Density % sol: 63.47 %
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: 2.95→19.944 Å / Num. obs: 46032 / % possible obs: 98.9 % / Redundancy: 10.6 % / Net I/σ(I): 1.87
Reflection shellResolution: 2.95→3.05 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFN

3ffn


Resolution: 2.95→19.944 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2386 5.18 %
Rwork0.1933 --
obs0.1962 46032 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→19.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11005 0 0 0 11005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111243
X-RAY DIFFRACTIONf_angle_d1.36715221
X-RAY DIFFRACTIONf_dihedral_angle_d8.8366672
X-RAY DIFFRACTIONf_chiral_restr0.0751620
X-RAY DIFFRACTIONf_plane_restr0.0092003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9502-3.01020.36141500.27962383X-RAY DIFFRACTION94
3.0102-3.07550.30751460.23572501X-RAY DIFFRACTION98
3.0755-3.14670.28491390.22372539X-RAY DIFFRACTION99
3.1467-3.22510.2961300.22842539X-RAY DIFFRACTION100
3.2251-3.31190.32921450.21672549X-RAY DIFFRACTION100
3.3119-3.40890.2751500.21752556X-RAY DIFFRACTION100
3.4089-3.51840.2861280.20582562X-RAY DIFFRACTION100
3.5184-3.64340.30461240.22722553X-RAY DIFFRACTION99
3.6434-3.78830.25431150.2112579X-RAY DIFFRACTION99
3.7883-3.95950.23171510.18492553X-RAY DIFFRACTION99
3.9595-4.16640.24971400.17942571X-RAY DIFFRACTION100
4.1664-4.42480.19911370.15862609X-RAY DIFFRACTION100
4.4248-4.76210.18661440.14182569X-RAY DIFFRACTION99
4.7621-5.23350.2121490.16592606X-RAY DIFFRACTION99
5.2335-5.97290.25261500.19722626X-RAY DIFFRACTION100
5.9729-7.45920.2641390.20562645X-RAY DIFFRACTION99
7.4592-19.94460.22311490.18972706X-RAY DIFFRACTION97
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)
10.6809-0.26920.50980.9791-0.09392.73370.00590.1108-0.0834-0.04370.0507-0.0016-0.06370.1982-0.06020.1955-0.0192-0.00710.3289-0.01170.378154.4046-27.125158.6948
21.0777-0.43280.12663.1824-0.19820.7068-0.07160.21350.0043-0.67810.01620.6011-0.0582-0.05470.04950.5295-0.0714-0.19780.33390.02180.502733.8176-0.775544.7896
31.7177-0.01830.01320.95630.05112.41740.01240.14280.3362-0.17020.0190.0581-0.0328-0.1241-0.05660.2569-0.0114-0.04590.26950.07310.3826-24.5148-42.112141.6382
41.95810.2772-0.88470.6417-0.03892.28590.0627-0.0564-0.07050.0075-0.017-0.0352-0.06990.3613-0.03480.2626-0.0274-0.01240.35190.05020.3642-12.4815-49.638448.5211
52.52971.70870.24491.7703-0.04050.4546-0.02580.39830.3343-0.1044-0.01040.06280.03430.010.07260.38030.03610.03920.57820.02430.4458-3.6083-38.900830.9257
62.3601-0.4186-0.15211.3998-0.17431.4605-0.00160.36850.2251-0.21860.007-0.15180.0195-0.20060.02260.3289-0.02990.00660.34490.06840.279325.4984-36.303525.842
72.74370.1722-0.76141.38160.45012.4210.00070.2830.0165-0.1159-0.13230.0882-0.0105-0.2810.09240.28080.0146-0.02520.40860.03770.307110.3609-38.853133.7671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 392 )
2X-RAY DIFFRACTION2chain 'A' and (resid 393 through 753 )
3X-RAY DIFFRACTION3chain 'B' and (resid 30 through 111 )
4X-RAY DIFFRACTION4chain 'B' and (resid 112 through 341 )
5X-RAY DIFFRACTION5chain 'B' and (resid 342 through 410 )
6X-RAY DIFFRACTION6chain 'B' and (resid 411 through 579 )
7X-RAY DIFFRACTION7chain 'B' and (resid 580 through 754 )

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