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- PDB-4s10: Gelsolin nanobody shielding mutant plasma gelsolin from furin pro... -

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Basic information

Entry
Database: PDB / ID: 4s10
TitleGelsolin nanobody shielding mutant plasma gelsolin from furin proteolysis
Components
  • GELSOLIN NANOBODY
  • Gelsolin
KeywordsMETAL BINDING PROTEIN/IMMUNE SYSTEM / GELSOLIN-LIKE / ACTIN-BINDING / METAL BINDING PROTEIN-IMMUNE SYSTEM complex
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 / Immunoglobulins / Immunoglobulin-like / Sandwich ...Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.614 Å
AuthorsWongsantichon, J. / Robinson, R.C. / Gettemans, J.
CitationJournal: Hum.Mol.Genet. / Year: 2015
Title: An ER-directed gelsolin nanobody targets the first step in amyloid formation in a gelsolin amyloidosis mouse model.
Authors: Van Overbeke, W. / Wongsantichon, J. / Everaert, I. / Verhelle, A. / Zwaenepoel, O. / Loonchanta, A. / Burtnick, L.D. / De Ganck, A. / Hochepied, T. / Haigh, J. / Cuvelier, C. / Derave, W. / ...Authors: Van Overbeke, W. / Wongsantichon, J. / Everaert, I. / Verhelle, A. / Zwaenepoel, O. / Loonchanta, A. / Burtnick, L.D. / De Ganck, A. / Hochepied, T. / Haigh, J. / Cuvelier, C. / Derave, W. / Robinson, R.C. / Gettemans, J.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GELSOLIN NANOBODY
C: Gelsolin
B: GELSOLIN NANOBODY
D: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4326
Polymers50,3514
Non-polymers802
Water1,874104
1
A: GELSOLIN NANOBODY
C: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2163
Polymers25,1762
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-15 kcal/mol
Surface area10900 Å2
MethodPISA
2
B: GELSOLIN NANOBODY
D: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2163
Polymers25,1762
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-15 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.598, 46.334, 76.438
Angle α, β, γ (deg.)103.00, 92.03, 89.85
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody GELSOLIN NANOBODY


Mass: 13695.976 Da / Num. of mol.: 2 / Fragment: GELSOLIN NANOBODY
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: 11479.736 Da / Num. of mol.: 2 / Fragment: GELSOLIN DOMAIN 2 / Mutation: S226D, R228D
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion / Details: 30% PEG 1500, VAPOR DIFFUSION, temperature 288K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→20 Å / Num. all: 24832 / Num. obs: 14057 / % possible obs: 93.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.8
Reflection shellResolution: 2.63→2.72 Å / Redundancy: 1.7 % / Rmerge(I) obs: 13.6 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1432 / % possible all: 91.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.614→19.722 Å / SU ML: 0.42 / σ(F): 1.97 / Phase error: 33.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3125 633 4.51 %RANDOM
Rwork0.2234 ---
obs0.2275 14035 92.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.614→19.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 2 104 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013575
X-RAY DIFFRACTIONf_angle_d1.4024827
X-RAY DIFFRACTIONf_dihedral_angle_d15.7171315
X-RAY DIFFRACTIONf_chiral_restr0.056512
X-RAY DIFFRACTIONf_plane_restr0.007652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6136-2.81480.38031230.25652585258589
2.8148-3.09710.33371100.24982805280595
3.0971-3.5430.2811370.22992752275295
3.543-4.45530.32771190.2052644264491
4.4553-19.72250.2951440.2142616261691
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)
11.28930.45390.74242.69730.71981.30810.17620.2567-0.2289-0.0209-0.0585-0.10060.10420.02110.00060.29610.0226-0.00770.35660.00470.2406-21.19411.495210.4094
21.24760.1084-0.43921.2521-0.65732.0646-0.055-0.1180.158-0.01760.0490.11070.06370.16680.00010.24730.01380.01010.192-0.01270.24131.441422.001428.0083
31.10170.08750.85672.4194-1.11672.21860.082-0.0144-0.19660.0579-0.0085-0.13080.17920.06990.00030.2626-0.0183-0.03130.37390.00140.281-7.749634.712757.0175
41.4604-0.3698-0.07271.83231.092.046-0.00690.01840.10550.05850.0915-0.0498-0.0186-0.15140.00030.2635-0.02830.03180.19770.00790.2451-30.54945.138939.275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 127)
2X-RAY DIFFRACTION2(chain 'C' and resid 159 through 259)
3X-RAY DIFFRACTION3(chain 'B' and resid 1 through 126)
4X-RAY DIFFRACTION4(chain 'D' and resid 160 through 261)

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