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- PDB-5imk: Nanobody targeting human Vsig4 in Spacegroup C2 -

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Basic information

Entry
Database: PDB / ID: 5imk
TitleNanobody targeting human Vsig4 in Spacegroup C2
Components
  • Nanobody
  • V-set and immunoglobulin domain-containing protein 4
KeywordsIMMUNE SYSTEM / Nanobody / Complement Receptor / Vsig4 CRIg
Function / homology
Function and homology information


negative regulation of complement activation, alternative pathway / negative regulation of macrophage activation / complement component C3b binding / complement activation, alternative pathway / negative regulation of interleukin-2 production / negative regulation of T cell proliferation / protein-containing complex / membrane
Similarity search - Function
VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesCamelidae (mammal)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.227 Å
AuthorsWen, Y.
CitationJournal: Immunobiology / Year: 2017
Title: Structural evaluation of a nanobody targeting complement receptor Vsig4 and its cross reactivity
Authors: Wen, Y. / Ouyang, Z. / Schoonooghe, S. / Luo, S. / De Baetselier, P. / Lu, W. / Muyldermans, S. / Raes, G. / Zheng, F.
History
DepositionMar 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nanobody
A: V-set and immunoglobulin domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)39,2062
Polymers39,2062
Non-polymers00
Water8,125451
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-2 kcal/mol
Surface area11970 Å2
Unit cell
Length a, b, c (Å)126.791, 30.369, 84.297
Angle α, β, γ (deg.)90.00, 126.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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Components

#1: Antibody Nanobody


Mass: 14599.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Protein V-set and immunoglobulin domain-containing protein 4 / Protein Z39Ig


Mass: 24606.785 Da / Num. of mol.: 1 / Fragment: UNP residues 19-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIG4, CRIg, Z39IG, UNQ317/PRO362 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y279
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 1.66 Å3/Da / Density % sol: 25.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate tribasic dehydrate pH5.6, 20% 2-Propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.227→42.011 Å / Num. obs: 74605 / Redundancy: 6.2 % / Net I/σ(I): 11.93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.227→42.011 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 2000 2.68 %
Rwork0.1716 --
obs0.172 74570 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.227→42.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 0 451 2361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091957
X-RAY DIFFRACTIONf_angle_d1.2912654
X-RAY DIFFRACTIONf_dihedral_angle_d14.646707
X-RAY DIFFRACTIONf_chiral_restr0.242281
X-RAY DIFFRACTIONf_plane_restr0.007346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2272-1.25790.29281370.27914819X-RAY DIFFRACTION92
1.2579-1.2920.26841170.2374474X-RAY DIFFRACTION87
1.292-1.330.21461560.20935256X-RAY DIFFRACTION100
1.33-1.37290.21961290.20015220X-RAY DIFFRACTION100
1.3729-1.4220.21151510.18965216X-RAY DIFFRACTION100
1.422-1.47890.19211460.18285212X-RAY DIFFRACTION100
1.4789-1.54620.19331430.17455243X-RAY DIFFRACTION100
1.5462-1.62770.18371410.16795268X-RAY DIFFRACTION100
1.6277-1.72970.21611400.16955234X-RAY DIFFRACTION100
1.7297-1.86330.18191530.17035276X-RAY DIFFRACTION100
1.8633-2.05080.17911470.15675257X-RAY DIFFRACTION100
2.0508-2.34750.17961410.1665320X-RAY DIFFRACTION100
2.3475-2.95750.18291520.17515295X-RAY DIFFRACTION100
2.9575-42.0360.16491470.15945480X-RAY DIFFRACTION100

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