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- PDB-7p2b: Crystal structure of human gelsolin amyloid mutant A551P -

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Basic information

Entry
Database: PDB / ID: 7p2b
TitleCrystal structure of human gelsolin amyloid mutant A551P
ComponentsGelsolin
KeywordsSTRUCTURAL PROTEIN / Gelsolin protein / actin binding protein
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 / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBollati, M. / de Rosa, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Amyloidosis Foundation United States
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: A novel hotspot of gelsolin instability triggers an alternative mechanism of amyloid aggregation.
Authors: Bollati, M. / Diomede, L. / Giorgino, T. / Natale, C. / Fagnani, E. / Boniardi, I. / Barbiroli, A. / Alemani, R. / Beeg, M. / Gobbi, M. / Fakin, A. / Mastrangelo, E. / Milani, M. / ...Authors: Bollati, M. / Diomede, L. / Giorgino, T. / Natale, C. / Fagnani, E. / Boniardi, I. / Barbiroli, A. / Alemani, R. / Beeg, M. / Gobbi, M. / Fakin, A. / Mastrangelo, E. / Milani, M. / Presciuttini, G. / Gabellieri, E. / Cioni, P. / de Rosa, M.
History
DepositionJul 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gelsolin
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,53218
Polymers171,0872
Non-polymers1,44516
Water1,856103
1
A: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,38810
Polymers85,5441
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1448
Polymers85,5441
Non-polymers6007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.070, 170.070, 152.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 85543.727 Da / Num. of mol.: 2 / Mutation: A551P
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 15% glycerol, 2.0 M 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: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→19.91 Å / Num. obs: 44997 / % possible obs: 100 % / Redundancy: 27.3 % / Biso Wilson estimate: 77.07 Å2 / CC1/2: 1 / Net I/σ(I): 11.53
Reflection shellResolution: 3→3.08 Å / Num. unique obs: 3291 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFN

3ffn


Resolution: 3→19.91 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 2248 5 %
Rwork0.2129 42706 -
obs0.2154 44954 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.35 Å2 / Biso mean: 84.4331 Å2 / Biso min: 46.16 Å2
Refinement stepCycle: final / Resolution: 3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11135 0 84 105 11324
Biso mean--88.98 64.88 -
Num. residues----1426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.060.42451370.357726032740
3.07-3.140.3821380.326326182756
3.14-3.210.36571390.299726512790
3.21-3.30.32891380.290426222760
3.3-3.40.30941390.278726342773
3.4-3.510.35531380.254826262764
3.51-3.630.3321400.23526582798
3.63-3.780.26581390.217126342773
3.78-3.950.25011400.207726532793
3.95-4.150.27441400.198526692809
4.15-4.410.22861400.178626502790
4.41-4.750.23531420.162126962838
4.75-5.220.24991410.183626732814
5.22-5.950.24991430.209827112854
5.96-7.430.28581440.213527502894
7.43-19.910.17541500.182628583008
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)
11.14940.20320.13490.35960.23930.64450.03570.1599-0.156-0.0769-0.03520.0053-0.0632-0.1434-0.00950.54260.035600.5078-0.030.646214.807244.9986-23.7959
20.42990.22070.19432.14320.73630.2086-0.0189-0.0765-0.04850.2350.0440.03620.054-0.0315-0.03580.54590.0082-0.03480.52550.04420.560342.492887.023138.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 754)A29 - 754
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 754)B29 - 754

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