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- PDB-9ezv: Structure of the single-domain antibody VHH_h2 in complex with hu... -

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Basic information

Entry
Database: PDB / ID: 9ezv
TitleStructure of the single-domain antibody VHH_h2 in complex with human Vsig4
Components
  • V-set and immunoglobulin domain-containing protein 4
  • single-domain antibody VHH_h2
KeywordsIMMUNE SYSTEM / VHH / nanobody / in silico / antibody / complex / single-domain
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMarkovic, I. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: To Be Published
Title: Structure of the single-domain antibody VHH_h1 in complex with human Vsig4
Authors: Markovic, I. / Savvides, S.N.
History
DepositionApr 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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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: single-domain antibody VHH_h2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,82211
Polymers29,2652
Non-polymers5579
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.291, 53.069, 87.531
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein V-set and immunoglobulin domain-containing protein 4 / Protein Z39Ig


Mass: 14486.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Immunoglobulin V-set domain / Source: (gene. exp.) Homo sapiens (human) / Gene: VSIG4, CRIg, Z39IG, UNQ317/PRO362 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y279
#2: Antibody single-domain antibody VHH_h2


Mass: 14779.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: single-domain antibody / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0,1M Na-citrate pH 5,6 20% 2-propanol 21% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.45→53.07 Å / Num. obs: 43885 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 20.07 Å2 / CC1/2: 1 / Rrim(I) all: 0.088 / Net I/σ(I): 17.77
Reflection shellResolution: 1.45→1.54 Å / Num. unique obs: 7006 / CC1/2: 0.423

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→33.76 Å / SU ML: 0.1849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 2000 4.56 %
Rwork0.1737 41871 -
obs0.1755 43871 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.74 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 36 178 2120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242026
X-RAY DIFFRACTIONf_angle_d0.61872741
X-RAY DIFFRACTIONf_chiral_restr0.0698285
X-RAY DIFFRACTIONf_plane_restr0.004363
X-RAY DIFFRACTIONf_dihedral_angle_d5.8935287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.34331370.29762956X-RAY DIFFRACTION99.81
1.49-1.530.3081460.24742948X-RAY DIFFRACTION99.94
1.53-1.570.30341420.22422935X-RAY DIFFRACTION99.94
1.57-1.620.25631380.21442956X-RAY DIFFRACTION99.55
1.62-1.680.3141370.21242932X-RAY DIFFRACTION99.42
1.68-1.750.24321440.18342964X-RAY DIFFRACTION100
1.75-1.830.22571440.17092971X-RAY DIFFRACTION100
1.83-1.920.18511420.15492968X-RAY DIFFRACTION100
1.92-2.040.20091440.14372983X-RAY DIFFRACTION100
2.04-2.20.21891460.15592992X-RAY DIFFRACTION99.94
2.2-2.420.20381400.16442993X-RAY DIFFRACTION99.81
2.42-2.770.23821460.17293028X-RAY DIFFRACTION100
2.77-3.490.18261480.17253052X-RAY DIFFRACTION99.94
3.49-33.760.20361460.17063193X-RAY DIFFRACTION99.88

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