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- PDB-9ezw: Structure of the single-domain antibody VHH_h3 in complex with hu... -

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Basic information

Entry
Database: PDB / ID: 9ezw
TitleStructure of the single-domain antibody VHH_h3 in complex with human Vsig4
Components
  • V-set and immunoglobulin domain-containing protein 4
  • single-domain antibody VHH_h3
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
DI(HYDROXYETHYL)ETHER / V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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_h3
C: V-set and immunoglobulin domain-containing protein 4
D: single-domain antibody VHH_h3
E: V-set and immunoglobulin domain-containing protein 4
F: single-domain antibody VHH_h3
G: V-set and immunoglobulin domain-containing protein 4
H: single-domain antibody VHH_h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,85319
Polymers117,1268
Non-polymers72711
Water9,350519
1
A: V-set and immunoglobulin domain-containing protein 4
B: single-domain antibody VHH_h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4064
Polymers29,2812
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: V-set and immunoglobulin domain-containing protein 4
D: single-domain antibody VHH_h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3443
Polymers29,2812
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: V-set and immunoglobulin domain-containing protein 4
F: single-domain antibody VHH_h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4685
Polymers29,2812
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: V-set and immunoglobulin domain-containing protein 4
H: single-domain antibody VHH_h3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6367
Polymers29,2812
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.867, 129.941, 144.284
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.: 4
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
single-domain antibody VHH_h3


Mass: 14795.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 294 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: Jul 15, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→129.94 Å / Num. obs: 89487 / % possible obs: 98.3 % / Redundancy: 13.9 % / Biso Wilson estimate: 30.72 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.61
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 14083 / CC1/2: 0.456

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→64.97 Å / SU ML: 0.2565 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 8947 10 %
Rwork0.1904 80528 -
obs0.1942 89475 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7712 0 47 519 8278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00698039
X-RAY DIFFRACTIONf_angle_d0.871710913
X-RAY DIFFRACTIONf_chiral_restr0.05851146
X-RAY DIFFRACTIONf_plane_restr0.00751442
X-RAY DIFFRACTIONf_dihedral_angle_d7.06851133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.38822920.35962622X-RAY DIFFRACTION98.65
1.92-1.940.33042940.30382666X-RAY DIFFRACTION98.57
1.94-1.970.32822970.28752672X-RAY DIFFRACTION98.05
1.97-1.990.33452900.27812605X-RAY DIFFRACTION97.64
1.99-2.020.31072760.27942487X-RAY DIFFRACTION91.55
2.02-2.050.31552850.26942555X-RAY DIFFRACTION95.37
2.05-2.080.30532940.24372654X-RAY DIFFRACTION98.73
2.08-2.110.29472970.2372671X-RAY DIFFRACTION98.87
2.11-2.140.28282970.22992677X-RAY DIFFRACTION98.94
2.14-2.170.30093020.2352714X-RAY DIFFRACTION99.02
2.17-2.210.27692930.23662646X-RAY DIFFRACTION98.96
2.21-2.250.28942990.21772687X-RAY DIFFRACTION98.97
2.25-2.30.27672960.20982658X-RAY DIFFRACTION98.99
2.3-2.340.25923040.2142734X-RAY DIFFRACTION99.31
2.34-2.390.28612940.21482652X-RAY DIFFRACTION99.33
2.39-2.450.27473010.2072712X-RAY DIFFRACTION99.08
2.45-2.510.24293000.19492695X-RAY DIFFRACTION99.57
2.51-2.580.24962990.19392692X-RAY DIFFRACTION99.27
2.58-2.650.25953030.20122721X-RAY DIFFRACTION99.41
2.65-2.740.26262970.19852681X-RAY DIFFRACTION98.97
2.74-2.840.23742970.19722664X-RAY DIFFRACTION97.56
2.84-2.950.24352790.19392521X-RAY DIFFRACTION91.86
2.95-3.090.24663020.19662718X-RAY DIFFRACTION99.83
3.09-3.250.2213050.17972738X-RAY DIFFRACTION99.87
3.25-3.450.20793050.18142749X-RAY DIFFRACTION99.93
3.45-3.720.19513070.17312757X-RAY DIFFRACTION99.97
3.72-4.090.19593090.15952783X-RAY DIFFRACTION100
4.09-4.680.15953100.13372789X-RAY DIFFRACTION99.77
4.68-5.90.16692950.15012661X-RAY DIFFRACTION94.59
5.9-64.970.19653280.18692947X-RAY DIFFRACTION99.57

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