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- PDB-9ezh: Structure of single-domain antibody VHH_h4 in complex with human Vsig4 -

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Basic information

Entry
Database: PDB / ID: 9ezh
TitleStructure of single-domain antibody VHH_h4 in complex with human Vsig4
Components
  • V-set and immunoglobulin domain-containing protein 4
  • VHH_h4
KeywordsIMMUNE SYSTEM / Nanobody / Mutations / CDR2 / CDR3 / hVsig4 / B7 family / immune regulatory proteins
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: 1.94 Å
AuthorsVizarraga, D. / Cianferoni, D. / Delgado, J. / van der Kant, R. / Garcia, T. / Maragkou, K. / Zhang, Z. / Dewilde, M. / Schymkowitz, J. / Rousseau, F. / Serrano, L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)JDC2022-048697-I Spain
CitationJournal: To be published
Title: In silico design of stable single-domain antibodies against multiple targets.
Authors: van der Kant, R. / Zhang, Z. / Markovic, I. / Vizarraga, D. / Garcia, T. / Maragkou, K. / Delgado, J. / Cianferoni, D. / Orlando, G. / Carolis, C. / Savvides, S. / N.Volkov, A. / Dewilde, M. ...Authors: van der Kant, R. / Zhang, Z. / Markovic, I. / Vizarraga, D. / Garcia, T. / Maragkou, K. / Delgado, J. / Cianferoni, D. / Orlando, G. / Carolis, C. / Savvides, S. / N.Volkov, A. / Dewilde, M. / Schymkowitz, J. / Serrano, L. / Rousseau, F.
History
DepositionApr 12, 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: VHH_h4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9163
Polymers26,8242
Non-polymers921
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-0 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.764, 50.961, 175.238
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: 13444.121 Da / Num. of mol.: 1
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 VHH_h4


Mass: 13379.732 Da / Num. of mol.: 1
Mutation: R51G, W52P, N53F, S56H, D101N, K102R, S105F, S106Y, F107D and E110N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0,1M Bis-Tris pH 6.0 and 24% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.938→87.619 Å / Num. obs: 18076 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 16
Reflection shellResolution: 1.938→1.971 Å / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 928 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→48.93 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 830 4.6 %
Rwork0.1943 --
obs0.1963 18055 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 6 117 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.057
X-RAY DIFFRACTIONf_dihedral_angle_d6.71280
X-RAY DIFFRACTIONf_chiral_restr0.066281
X-RAY DIFFRACTIONf_plane_restr0.009360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.060.30931240.24082814X-RAY DIFFRACTION100
2.06-2.220.25861300.22442806X-RAY DIFFRACTION100
2.22-2.440.25461310.212827X-RAY DIFFRACTION100
2.44-2.790.28341410.21392859X-RAY DIFFRACTION100
2.79-3.520.24071410.18962870X-RAY DIFFRACTION100
3.52-48.930.2151630.17773049X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.1082 Å / Origin y: -9.2444 Å / Origin z: 22.6379 Å
111213212223313233
T0.39 Å20.0706 Å2-0.031 Å2-0.3078 Å20.023 Å2--0.271 Å2
L1.4033 °2-0.3097 °2-0.4823 °2-3.1704 °21.1322 °2--3.7641 °2
S0.1366 Å °0.3822 Å °0.1381 Å °-0.7113 Å °-0.2051 Å °0.1297 Å °-0.7884 Å °-0.2395 Å °0.0316 Å °
Refinement TLS groupSelection details: all

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