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- PDB-4s11: Gelsolin nanobody shielding mutant plasma gelsolin from furin pro... -

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Basic information

Entry
Database: PDB / ID: 4s11
TitleGelsolin nanobody shielding mutant plasma gelsolin from furin proteolysis
ComponentsGELSOLIN NANOBODY
KeywordsIMMUNE SYSTEM / NANOBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsWongsantichon, J. / Loonchanta, A. / 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
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)14,1101
Polymers14,1101
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.633, 56.299, 57.449
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


Mass: 14110.416 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.2
Details: 40% PEG 8000, 0.1M HEPES, pH 8.2, VAPOR DIFFUSION, temperature 277K

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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: Oct 12, 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→20 Å / Num. obs: 7828 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 8.1 / Num. unique all: 371 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.998→18.13 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 385 4.95 %RANDOM
Rwork0.1587 ---
obs0.1611 7783 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.998→18.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 0 57 1039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081004
X-RAY DIFFRACTIONf_angle_d1.1211356
X-RAY DIFFRACTIONf_dihedral_angle_d12.445357
X-RAY DIFFRACTIONf_chiral_restr0.042142
X-RAY DIFFRACTIONf_plane_restr0.005181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9983-2.2870.2151220.15032396239699
2.287-2.87950.26751130.181124632463100
2.8795-18.13030.18341500.151325392539100
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)
10.4866-0.1780.03546.6633-0.87211.4402-0.0814-0.1352-0.08330.07140.31970.45060.0459-0.0838-0.19150.1575-0.00370.0030.1904-0.0290.1739-20.4128-5.7102-7.9047
21.81040.71530.59881.7551-1.00212.19240.11310.18460.2845-0.2404-0.0060.0836-0.0788-0.1421-0.08360.22460.03750.04850.270.06120.1871-19.70437.9502-12.6726
32.76650.9092-0.7981.8802-0.06591.2449-0.104-0.01110.0559-0.0464-0.0209-0.0661-0.00120.08270.09050.1560.00760.00570.1320.00850.1513-14.06813.9956-0.5454
41.10110.3938-0.45461.84750.39180.8581-0.0289-0.00070.0520.0639-0.0324-0.08420.06980.04670.09020.15220.0141-0.00790.1770.01630.1676-13.2014-1.7025-4.7912
53.63581.7513-0.84671.6990.95862.3787-0.153-0.3180.63210.1840.21760.15450.25080.1284-0.02540.1527-0.0249-0.03670.2423-0.01070.2541-12.630715.2951-1.1369
63.07151.468-1.09587.248-0.71630.6366-0.0942-0.1180.2121-0.18370.06010.4074-0.1733-0.22080.05980.15840.02160.02930.1840.03940.1807-22.23358.9849-0.5159
70.16740.1298-0.05320.1018-0.01740.39810.2141-0.0905-0.53070.00380.01950.4433-0.0271-0.0348-0.0840.14030.0020.00320.19430.05090.2637-18.4132-17.5961-0.3412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 32 )
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 130 )

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