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- PDB-9ezu: Structure of the single-domain antibody VHH_h1 in complex with hu... -

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Basic information

Entry
Database: PDB / ID: 9ezu
TitleStructure of the single-domain antibody VHH_h1 in complex with human Vsig4
Components
  • V-set and immunoglobulin domain-containing protein 4
  • single-domain antibody VHH_h1
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
V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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

Downloads & links

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Assembly

Deposited unit
A: V-set and immunoglobulin domain-containing protein 4
B: single-domain antibody VHH_h1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4533
Polymers29,3572
Non-polymers961
Water4,576254
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)50.651, 51.404, 89.649
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_h1


Mass: 14870.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Single-domain antibody / Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 0,17M ammonium sulfate 15% glycerol 25,5% 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: Sep 21, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.05→51.4 Å / Num. obs: 109581 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.1 / Net I/σ(I): 12.4
Reflection shellResolution: 1.05→1.11 Å / Num. unique obs: 17482 / CC1/2: 0.757 / Rrim(I) all: 1.02

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→24.71 Å / SU ML: 0.0922 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1757 9980 9.11 %
Rwork0.1565 99590 -
obs0.1583 109570 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.06 Å2
Refinement stepCycle: LAST / Resolution: 1.05→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 5 254 2190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01192134
X-RAY DIFFRACTIONf_angle_d1.2512916
X-RAY DIFFRACTIONf_chiral_restr0.1075300
X-RAY DIFFRACTIONf_plane_restr0.0098394
X-RAY DIFFRACTIONf_dihedral_angle_d7.058306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.3043130.28353264X-RAY DIFFRACTION98.78
1.06-1.070.26643380.23213280X-RAY DIFFRACTION99.61
1.07-1.090.22973110.21443254X-RAY DIFFRACTION99.86
1.09-1.10.20513370.1963286X-RAY DIFFRACTION99.92
1.1-1.120.19253300.17873275X-RAY DIFFRACTION99.92
1.12-1.130.18633260.1643288X-RAY DIFFRACTION99.97
1.13-1.150.16993340.16653310X-RAY DIFFRACTION99.95
1.15-1.160.17793280.15923274X-RAY DIFFRACTION99.94
1.16-1.180.16953290.1583290X-RAY DIFFRACTION100
1.18-1.20.17363300.15963292X-RAY DIFFRACTION99.94
1.2-1.220.17033410.15223299X-RAY DIFFRACTION99.97
1.22-1.250.17173240.15583278X-RAY DIFFRACTION99.86
1.25-1.270.18523320.15773287X-RAY DIFFRACTION99.94
1.27-1.290.18113300.14483296X-RAY DIFFRACTION99.94
1.29-1.320.1673360.13983316X-RAY DIFFRACTION99.97
1.32-1.350.18053330.14293304X-RAY DIFFRACTION99.95
1.35-1.390.17413330.14573293X-RAY DIFFRACTION100
1.39-1.430.15163300.14513310X-RAY DIFFRACTION100
1.43-1.470.15873240.1423327X-RAY DIFFRACTION100
1.47-1.510.15593300.13583323X-RAY DIFFRACTION100
1.51-1.570.15553380.1323301X-RAY DIFFRACTION99.95
1.57-1.630.15713330.13583324X-RAY DIFFRACTION100
1.63-1.710.16033380.14423306X-RAY DIFFRACTION100
1.71-1.80.17713340.14623352X-RAY DIFFRACTION100
1.8-1.910.17143380.14843355X-RAY DIFFRACTION100
1.91-2.060.15943390.14683360X-RAY DIFFRACTION100
2.06-2.260.16943340.1483359X-RAY DIFFRACTION100
2.26-2.590.19063390.16523392X-RAY DIFFRACTION99.97
2.59-3.260.19793390.17133423X-RAY DIFFRACTION99.97
3.26-24.710.16883590.15973572X-RAY DIFFRACTION99.95

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