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- PDB-6h1f: Structure of the nanobody-stabilized gelsolin D187N variant (seco... -

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Basic information

Entry
Database: PDB / ID: 6h1f
TitleStructure of the nanobody-stabilized gelsolin D187N variant (second domain)
Components
  • Gelsolin
  • gelsolin nanobody, Nb11
KeywordsSTRUCTURAL PROTEIN / Amyloidosis / calcium / misfolding / nanobody / mutation
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
THIOCYANATE ION / Gelsolin
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHassan, A. / Milani, M. / Mastrangelo, E. / de Rosa, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Amyloidosis Foundation United States
CitationJournal: Biochim Biophys Acta Mol Basis Dis / Year: 2019
Title: Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant.
Authors: Giorgino, T. / Mattioni, D. / Hassan, A. / Milani, M. / Mastrangelo, E. / Barbiroli, A. / Verhelle, A. / Gettemans, J. / Barzago, M.M. / Diomede, L. / de Rosa, M.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 nanobody, Nb11
B: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4913
Polymers28,4322
Non-polymers581
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.859, 46.835, 132.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody gelsolin nanobody, Nb11


Mass: 15266.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Gelsolin / / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 13165.664 Da / Num. of mol.: 1 / Mutation: D187N
Source method: isolated from a genetically manipulated source
Details: second domain (G2) of gelsolin pathological variant D187N
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Potassium thiocyanate, 30%w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0062 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2018 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0062 Å / Relative weight: 1
ReflectionResolution: 1.9→46.83 Å / Num. obs: 17289 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1078 / CC1/2: 0.714 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S10

4s10


Resolution: 1.9→44.143 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2333 1724 10 %
Rwork0.1989 --
obs0.2024 17239 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 3 111 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061823
X-RAY DIFFRACTIONf_angle_d0.7862471
X-RAY DIFFRACTIONf_dihedral_angle_d23.32681
X-RAY DIFFRACTIONf_chiral_restr0.055263
X-RAY DIFFRACTIONf_plane_restr0.008332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95590.27141400.26251262X-RAY DIFFRACTION100
1.9559-2.01910.31661410.25111264X-RAY DIFFRACTION100
2.0191-2.09120.31021400.2491267X-RAY DIFFRACTION100
2.0912-2.17490.32571410.23641264X-RAY DIFFRACTION100
2.1749-2.27390.27551420.22721284X-RAY DIFFRACTION100
2.2739-2.39380.23541430.20671280X-RAY DIFFRACTION100
2.3938-2.54380.27091420.21971280X-RAY DIFFRACTION100
2.5438-2.74010.26661430.22251289X-RAY DIFFRACTION100
2.7401-3.01580.27041430.21861285X-RAY DIFFRACTION99
3.0158-3.45210.22991460.18351310X-RAY DIFFRACTION100
3.4521-4.34870.18271470.15881327X-RAY DIFFRACTION100
4.3487-44.1550.19131560.18561403X-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)
12.5001-1.19772.17632.4654-1.75147.0134-0.4718-0.45050.13560.60150.5060.2083-1.1366-0.7104-0.04580.47040.15650.03820.45750.08010.4963-24.826423.5587-25.7883
21.3892-0.2759-0.23141.7313-0.35622.78130.03740.0785-0.0216-0.04370.34470.4007-0.1028-0.3696-0.27740.36930.00260.02860.3050.08270.3222-16.857514.5672-18.1011
37.3259-1.85690.05361.0864-0.85131.09960.4002-0.455-1.6364-0.05270.0040.58550.4132-0.5824-0.3940.4033-0.0645-0.11220.33520.0680.5977-24.93839.7309-29.0273
45.96120.1273.59414.9927-0.54882.2561-0.00730.7308-0.2505-0.8366-0.0709-0.10460.24190.85190.06560.39550.032-0.01990.36650.03770.3164-11.281213.3929-29.4493
56.9008-1.5321-2.06767.25470.21076.1065-0.0233-0.40970.60080.18320.3198-0.50710.19680.5367-0.320.3730.0187-0.08710.3123-0.01680.3682-15.250221.7748-27.1127
60.8133-0.90291.53333.3792-3.44263.70950.06440.0652-0.195-0.38930.36010.6210.2598-0.2307-0.4220.3316-0.0215-0.06010.2590.01730.3153-19.100912.0356-26.9182
74.2998-4.0333.54255.4054-2.89124.2331-0.1591-0.1595-0.38420.02270.6511.0093-0.1341-0.6812-0.47560.2348-0.0171-0.03220.4960.19050.4386-26.477614.1156-25.0493
88.9929-1.00790.18711.557-0.06141.55070.2294-0.7182-0.6707-0.0257-0.05760.20160.1437-0.2139-0.1580.2786-0.0622-0.05150.27380.03990.2534-7.916-4.9347-3.8252
93.31-0.7620.16631.0548-0.3592.69390.1349-0.3244-0.29970.1088-0.1001-0.09-0.01010.2733-0.03820.249-0.0458-0.06790.20580.04150.2478-1.1807-2.4837-5.3358
109.2522-0.66191.49881.9475-0.68462.35460.31560.7172-1.2296-0.2626-0.11940.24830.38090.0131-0.18470.37040.021-0.08890.2631-0.08760.4097-4.8749-9.4221-13.9583
111.37720.21641.01971.55270.55372.21750.1124-0.0779-0.05330.0012-0.0837-0.10540.00360.067-0.02430.22-0.014-0.00310.2398-0.02820.2503-3.11325.9448-7.4263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 64 )
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 83 )
6X-RAY DIFFRACTION6chain 'A' and (resid 84 through 110 )
7X-RAY DIFFRACTION7chain 'A' and (resid 111 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 157 through 167 )
9X-RAY DIFFRACTION9chain 'B' and (resid 168 through 206 )
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 229 )
11X-RAY DIFFRACTION11chain 'B' and (resid 230 through 258 )

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