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- PDB-5iml: Nanobody targeting human Vsig4 in Spacegroup P212121 -

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Basic information

Entry
Database: PDB / ID: 5iml
TitleNanobody targeting human Vsig4 in Spacegroup P212121
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 speciesHomo sapiens (human)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 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: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Database references / Category: citation / diffrn_detector
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _diffrn_detector.detector
Revision 1.2Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,2062
Polymers39,2062
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-2 kcal/mol
Surface area11770 Å2
Unit cell
Length a, b, c (Å)29.269, 50.048, 160.648
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: 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
#2: 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.5 Å3/Da / Density % sol: 18.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: (1) 1.2M sodium citrate tribasic dehydrate, 0.1M BIS-TRIS propane pH7.0 and (2) 0.17M Ammonium sulfate, 15% Glycerol, 25.5% 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: 1.8→47.78 Å / Num. obs: 22570 / % possible obs: 99.49 % / Redundancy: 9.8 % / Net I/σ(I): 12.79

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.8→47.78 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.2261 2000 8.86 %
Rwork0.1811 --
obs0.1852 22567 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 0 178 2098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151967
X-RAY DIFFRACTIONf_angle_d1.5082666
X-RAY DIFFRACTIONf_dihedral_angle_d16.541713
X-RAY DIFFRACTIONf_chiral_restr0.06281
X-RAY DIFFRACTIONf_plane_restr0.008348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8035-1.84860.34051310.29461348X-RAY DIFFRACTION93
1.8486-1.89850.32251380.25871422X-RAY DIFFRACTION100
1.8985-1.95440.29131430.25171464X-RAY DIFFRACTION100
1.9544-2.01750.26251390.20641441X-RAY DIFFRACTION100
2.0175-2.08960.27271450.2111482X-RAY DIFFRACTION100
2.0896-2.17330.23281380.19211421X-RAY DIFFRACTION100
2.1733-2.27220.28681440.19981470X-RAY DIFFRACTION100
2.2722-2.3920.23981400.19061451X-RAY DIFFRACTION100
2.392-2.54180.28861420.19291463X-RAY DIFFRACTION100
2.5418-2.73810.25571440.18851483X-RAY DIFFRACTION100
2.7381-3.01360.22471440.18581474X-RAY DIFFRACTION100
3.0136-3.44950.21971450.17331494X-RAY DIFFRACTION100
3.4495-4.34560.17851490.14621531X-RAY DIFFRACTION100
4.3456-47.79960.18241580.16181623X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.9195 Å / Origin y: -9.6314 Å / Origin z: 21.8292 Å
111213212223313233
T0.1763 Å2-0.0217 Å20.0167 Å2-0.1447 Å20.0006 Å2--0.1951 Å2
L1.0259 °2-0.2485 °20.6921 °2-0.348 °2-0.0878 °2--1.4285 °2
S-0.0087 Å °0.0508 Å °-0.017 Å °0.0624 Å °-0.0046 Å °-0.0147 Å °-0.006 Å °-0.0064 Å °0.0124 Å °
Refinement TLS groupSelection details: all

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