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- PDB-6qw3: Calcium-bound gelsolin domain 2 -

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Basic information

Entry
Database: PDB / ID: 6qw3
TitleCalcium-bound gelsolin domain 2
ComponentsGelsolin
KeywordsSTRUCTURAL PROTEIN / amyloidosis / gelsolin / actin-binding
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 / 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: 1.3 Å
AuthorsScalone, E. / Boni, F. / Milani, M. / Mastrangelo, E. / de Rosa, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Amyloidosis Foundation United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion.
Authors: Bollati, M. / Scalone, E. / Boni, F. / Mastrangelo, E. / Giorgino, T. / Milani, M. / de Rosa, M.
History
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)13,2072
Polymers13,1671
Non-polymers401
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area6490 Å2
Unit cell
Length a, b, c (Å)26.653, 50.275, 70.819
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-434-

HOH

21A-458-

HOH

31A-514-

HOH

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Components

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


Mass: 13166.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: gelsolin domain 2 (G2) / Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.8 Å3/Da / Density % sol: 31.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 36% PEG5000 MME, 0.1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→70.82 Å / Num. obs: 24096 / % possible obs: 99.5 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.023 / Rrim(I) all: 0.08 / Net I/σ(I): 14
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1103 / CC1/2: 0.579 / Rpim(I) all: 0.409 / Rrim(I) all: 0.874 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KCQ

1kcq


Resolution: 1.3→40.995 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 1999 8.31 %10%
Rwork0.1538 ---
obs0.1556 24046 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→40.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 1 150 1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016975
X-RAY DIFFRACTIONf_angle_d1.4691337
X-RAY DIFFRACTIONf_dihedral_angle_d29.627404
X-RAY DIFFRACTIONf_chiral_restr0.108142
X-RAY DIFFRACTIONf_plane_restr0.009184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3002-1.33270.26621340.24021480X-RAY DIFFRACTION94
1.3327-1.36870.25941360.22431503X-RAY DIFFRACTION99
1.3687-1.4090.24331430.20391573X-RAY DIFFRACTION100
1.409-1.45450.20611390.19231543X-RAY DIFFRACTION100
1.4545-1.50650.17521410.1711559X-RAY DIFFRACTION100
1.5065-1.56680.21841430.16061572X-RAY DIFFRACTION100
1.5668-1.63810.17921410.16081558X-RAY DIFFRACTION100
1.6381-1.72440.1821430.1541568X-RAY DIFFRACTION100
1.7244-1.83250.18251420.15361571X-RAY DIFFRACTION100
1.8325-1.9740.17281440.15861585X-RAY DIFFRACTION100
1.974-2.17260.17111440.14331586X-RAY DIFFRACTION100
2.1726-2.4870.1591460.14681603X-RAY DIFFRACTION100
2.487-3.13310.18931470.15591623X-RAY DIFFRACTION100
3.1331-41.01530.1521560.13911723X-RAY DIFFRACTION100
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)
15.0489-1.1561-0.72954.91240.8045.20480.18180.26870.012-0.5127-0.1501-0.117-0.2102-0.1084-0.07140.1203-0.013300.09690.01670.098511.467815.95030.7136
20.3497-0.2755-0.33832.79190.84352.2714-0.0069-0.0235-0.02830.1135-0.02780.0947-0.0085-0.04720.02620.09980.00040.00010.1229-0.00490.124810.182314.49449.331
30.89960.5783-0.22596.83131.01381.559-0.0182-0.0186-0.0899-0.230.0844-0.5525-0.05420.1803-0.06680.1081-0.0050.00530.165-0.01850.153321.370516.57334.1244
43.4051.68311.01843.58431.37352.028-0.025-0.13670.2430.38910.0328-0.0786-0.48460.19490.0240.3136-0.0581-0.02130.1795-0.01480.153217.718632.66118.5774
58.81294.1649-0.83795.5805-2.85837.70040.1451-0.404-0.21110.4328-0.1473-0.3668-0.18890.40760.00950.0998-0.0073-0.03180.16630.00120.078616.839318.993115.7504
65.11120.47331.30569.54093.1226.88970.2062-0.253-0.36560.2316-0.23130.05581.0992-0.12570.0460.3295-0.041-0.00750.22320.03040.178810.724911.60818.596
78.50580.1626.25611.4241-2.25268.6335-0.0362-0.55250.08760.3326-0.1170.2091-0.4111-0.67520.17080.17610.00750.03590.1907-0.0080.17075.523719.177618.5173
81.0002-1.259-1.19921.73841.38581.6144-0.19560.0391-0.20980.2153-0.04950.35130.2584-0.20840.27170.1588-0.01050.03970.18660.00060.21573.87256.548511.3806
92.2322-0.0911-0.4690.6519-1.1452.1933-0.03220.27530.0652-0.3440.09030.004-0.46220.0239-0.05430.2588-0.02930.00150.1739-0.00650.129713.55123.9839-9.3797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 158 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 223 )
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 229 )
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 235 )
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 240 )
7X-RAY DIFFRACTION7chain 'A' and (resid 241 through 247 )
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 257 )
9X-RAY DIFFRACTION9chain 'A' and (resid 258 through 266 )

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