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- PDB-9sfx: Secukinumab Fv in complex with human IL-17A -

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Basic information

Entry
Database: PDB / ID: 9sfx
TitleSecukinumab Fv in complex with human IL-17A
Components
  • (Secukinumab Fv ...) x 2
  • Heavy-chain of anti-IL-17A antibody XAB5 Fv (crystallization aid)
  • Interleukin-17A
  • Light-chain of anti-IL-17A antibody XAB5 (crystallization aid)
KeywordsCYTOKINE / MONOCLONAL ANTIBODY / THERAPEUTIC ANTIBODY / FV FRAGMENT
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 / positive regulation of interleukin-1 beta production / cytokine activity / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRondeau, J.-M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2025
Title: IL-17A complexes with therapeutic antibodies exhibit distinct size distributions, potentially contributing to clinically observed immunogenicity.
Authors: Ungan, D. / Be, C. / Baczyk, P. / Mittermeier, S. / Lehmann, S. / Wiesmann, C. / Huber, T. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 21, 2025Deposition 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: Secukinumab Fv light-chain
B: Secukinumab Fv heavy-chain
C: Interleukin-17A
H: Heavy-chain of anti-IL-17A antibody XAB5 Fv (crystallization aid)
L: Light-chain of anti-IL-17A antibody XAB5 (crystallization aid)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4299
Polymers70,0605
Non-polymers3684
Water63135
1
A: Secukinumab Fv light-chain
B: Secukinumab Fv heavy-chain
C: Interleukin-17A
H: Heavy-chain of anti-IL-17A antibody XAB5 Fv (crystallization aid)
L: Light-chain of anti-IL-17A antibody XAB5 (crystallization aid)
hetero molecules

A: Secukinumab Fv light-chain
B: Secukinumab Fv heavy-chain
C: Interleukin-17A
H: Heavy-chain of anti-IL-17A antibody XAB5 Fv (crystallization aid)
L: Light-chain of anti-IL-17A antibody XAB5 (crystallization aid)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,85718
Polymers140,12010
Non-polymers7378
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Unit cell
Length a, b, c (Å)186.350, 186.350, 107.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules C

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


Mass: 15712.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct included amino acids 20 to 155 of human IL-17A with a N-terminal His6 tag followed by a PreScission cleavage site. The tag was cleaved with PreScission protease before ...Details: The construct included amino acids 20 to 155 of human IL-17A with a N-terminal His6 tag followed by a PreScission cleavage site. The tag was cleaved with PreScission protease before crystallisation of the complex with the secukinumab Fv
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q16552

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Antibody , 4 types, 4 molecules ABHL

#1: Antibody Secukinumab Fv light-chain


Mass: 12688.048 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct included a Strep tag (WSHPQFEK) fused with the carboxyterminus of the light-chain
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
#2: Antibody Secukinumab Fv heavy-chain


Mass: 15297.013 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct included a C-terminal His6 tag / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
#4: Antibody Heavy-chain of anti-IL-17A antibody XAB5 Fv (crystallization aid)


Mass: 13723.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct included a C-terminal His6 tag / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
#5: Antibody Light-chain of anti-IL-17A antibody XAB5 (crystallization aid)


Mass: 12639.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct included a C-terminal Strep tag (WSHPQFEK)
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1

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Non-polymers , 2 types, 39 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.86 Å3/Da / Density % sol: 68.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, 1.8M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.6→27.68 Å / Num. obs: 34093 / % possible obs: 99 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.134 / Net I/σ(I): 23.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.67212.8881.7324580.7022.95898.6
2.67-2.7420.982.2572.224050.7972.31298.7
2.74-2.8220.821.6383.0623380.8841.67898.6
2.82-2.9120.561.2114.0422800.9291.24198.7
2.91-320.070.9265.0722030.9460.9598.6
3-3.1119.340.6446.9121560.970.66199.1
3.11-3.2219.670.449.7120770.9870.45299.2
3.22-3.3620.850.32313.2419960.9930.33199.2
3.36-3.5120.690.2217.9919180.9970.22698.9
3.51-3.6820.440.15523.7818480.9980.15999.4
3.68-3.8819.90.1228.3517600.9980.12498.9
3.88-4.1119.130.08935.316740.9990.09299.5
4.11-4.3919.770.06645.315850.9990.06899.2
4.39-4.7520.410.05355.78147310.05599.2
4.75-5.220.080.05157.8136910.05299.5
5.2-5.8118.690.05452.9912530.9990.05599.5
5.81-6.7118.810.05352.3111190.9990.05599.5
6.71-8.2219.720.04263.2795010.04399.5
8.22-11.6317.70.0377.876410.03199.5
11.63-27.6815.940.0377.8146710.03198.7

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XSCALEJuly 4, 2012data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→27.68 Å / Cor.coef. Fo:Fc: 0.9393 / Cor.coef. Fo:Fc free: 0.9171 / SU R Cruickshank DPI: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1702 5 %RANDOM
Rwork0.1765 ---
obs0.1783 34046 99.03 %-
Displacement parametersBiso mean: 79.35 Å2
Baniso -1Baniso -2Baniso -3
1--9.7709 Å20 Å20 Å2
2---9.7709 Å20 Å2
3---19.5417 Å2
Refine analyzeLuzzati coordinate error obs: 0.383 Å
Refinement stepCycle: 1 / Resolution: 2.6→27.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 24 35 4444
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014521HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.26137HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1502SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes659HARMONIC5
X-RAY DIFFRACTIONt_it4521HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion19.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion564SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4782SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.68 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2616 144 5.01 %
Rwork0.2346 2728 -
all0.2359 2872 -
obs--99.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.54571.0715-0.05146.1087-0.7850.55810.0442-0.1074-0.05420.59780.03840.12360.29650.0013-0.08260.0233-0.154-0.0207-0.0591-0.0237-0.136733.6382-108.0025-6.3034
22.90750.3527-0.82624.28640.66264.9826-0.22750.47620.0851-0.19940.12940.6070.2834-0.57050.0981-0.1984-0.2058-0.07280.06910.0577-0.065928.5051-95.8443-24.3653
31.5758-0.9626-0.50660.99640.3681.94850.16640.0690.20090.10330.022-0.1055-0.5638-0.1945-0.1884-0.0368-0.05350.1364-0.04030.0662-0.089238.3932-63.4582-12.236
42.58120.8702-1.14723.9211-0.43775.60970.1903-0.26730.42710.6848-0.0539-0.0432-0.8652-0.1106-0.13640.0043-0.02860.1095-0.1058-0.0337-0.185830.2421-55.879516.1775
53.87860.2333-1.74145.7085-0.29484.00010.15520.50420.1666-0.3556-0.01610.9758-0.3003-1.4302-0.1391-0.3110.070.03810.27810.1005-0.237314.8096-60.56580.5728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ H|* }
5X-RAY DIFFRACTION5{ L|* }

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