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- PDB-7wkx: IL-17A in complex with the humanized antibody HB0017 -

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Basic information

Entry
Database: PDB / ID: 7wkx
TitleIL-17A in complex with the humanized antibody HB0017
Components
  • Heavy chain of HB0017 Fab
  • Interleukin-17A
  • Light chain of HB0017 Fab
KeywordsCYTOKINE / HB0017 / IL17A / monoclonal antibody / complex
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-1 beta production / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / innate immune response / external side of plasma membrane / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / MALONIC ACID / Interleukin-17A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsXu, J. / Zhu, X. / He, Y.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural and functional insights into a novel pre-clinical-stage antibody targeting IL-17A for treatment of autoimmune diseases.
Authors: Xu, J.G. / Jia, H. / Chen, S. / Xu, J. / Zhan, Y. / Yu, H. / Wang, W. / Kang, X. / Cui, X. / Feng, Y. / Chen, X. / Xu, W. / Pan, X. / Wei, X. / Li, H. / Wang, Y. / Xia, S. / Liu, X. / Yang, L. / He, Y. / Zhu, X.
History
DepositionJan 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of HB0017 Fab
B: Heavy chain of HB0017 Fab
C: Light chain of HB0017 Fab
D: Light chain of HB0017 Fab
E: Interleukin-17A
F: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,06317
Polymers129,0946
Non-polymers96911
Water66737
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)301.142, 50.829, 117.216
Angle α, β, γ (deg.)90.000, 101.270, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 217
2010B1 - 217
1020C1 - 215
2020D1 - 215
1030E24 - 130
2030F24 - 130

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules EF

#3: Protein Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 17427.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16552

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Antibody , 2 types, 4 molecules ABCD

#1: Antibody Heavy chain of HB0017 Fab


Mass: 23154.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light chain of HB0017 Fab


Mass: 23964.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 48 molecules

#4: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.41 Å3/Da / Density % sol: 63.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 4% v/v Tacsimate pH 7.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 1.03923 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 41319 / % possible obs: 96.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vxs,5drw

2vxs

5drw


Resolution: 2.81→45.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 14.379 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.686 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 1997 4.8 %RANDOM
Rwork0.2055 ---
obs0.2078 39322 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.99 Å2 / Biso mean: 62.423 Å2 / Biso min: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å22.13 Å2
2--1.37 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.81→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8147 0 65 37 8249
Biso mean--80.2 48.06 -
Num. residues----1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177389
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.64811515
X-RAY DIFFRACTIONr_angle_other_deg1.2761.57417266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.08151051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09823.263380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.293151297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5491530
X-RAY DIFFRACTIONr_chiral_restr0.0770.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029478
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021708
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A58910.14
12B58910.14
21C62650.15
22D62650.15
31E24000.18
32F24000.18
LS refinement shellResolution: 2.81→2.879 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.358 120 -
Rwork0.322 2364 -
obs--78.41 %

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