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- PDB-8dy1: Crystal Structure of scFv CAT2200 LH in complex with IL-17A -

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Basic information

Entry
Database: PDB / ID: 8dy1
TitleCrystal Structure of scFv CAT2200 LH in complex with IL-17A
Components
  • Interleukin-17A
  • scFv CAT2200 LH
KeywordsIMMUNE SYSTEM / scFv / stapled scFv / spFv / germline scFv / single chain Fv / scFv stabilizations / antibody / antibody antigen 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 / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
Model detailsCrystal Structure of spFv GLK1 in LH configuration
AuthorsLuo, J. / Armstrong, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mabs / Year: 2023
Title: "Stapling" scFv for multispecific biotherapeutics of superior properties.
Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / ...Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / Heyne, S. / Mazzanti, N. / Testa, J. / Diem, M.D. / Gorre, E. / Mahan, A. / Nanda, H. / Gunawardena, H.P. / Gervais, A. / Armstrong, A.A. / Teplyakov, A. / Huang, C. / Zwolak, A. / Chowdhury, P. / Cheung, W.C. / Luo, J.
History
DepositionAug 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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

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Assembly

Deposited unit
A: Interleukin-17A
B: Interleukin-17A
C: scFv CAT2200 LH
D: scFv CAT2200 LH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0368
Polymers81,6524
Non-polymers3844
Water1,31573
1
A: Interleukin-17A
C: scFv CAT2200 LH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0184
Polymers40,8262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-39 kcal/mol
Surface area16650 Å2
MethodPISA
2
B: Interleukin-17A
D: scFv CAT2200 LH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0184
Polymers40,8262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-38 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.930, 62.050, 111.710
Angle α, β, γ (deg.)90.000, 99.690, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 2 through 110 or resid 131...
21(chain D and (resid 2 through 110 or resid 131...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEU(chain C and (resid 2 through 110 or resid 131...CC2 - 1102 - 110
12GLUGLULEULEU(chain C and (resid 2 through 110 or resid 131...CC131 - 148131 - 148
13LEULEUVALVAL(chain C and (resid 2 through 110 or resid 131...CC150 - 194150 - 194
14GLYGLYSERSER(chain C and (resid 2 through 110 or resid 131...CC196 - 205196 - 205
15ASNASNSERSER(chain C and (resid 2 through 110 or resid 131...CC207 - 247207 - 247
21PHEPHELEULEU(chain D and (resid 2 through 110 or resid 131...DD2 - 1102 - 110
22GLUGLUGLYGLY(chain D and (resid 2 through 110 or resid 131...DD131 - 140131 - 140
23ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
24ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
25ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
26ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
27ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
28ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
29ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248

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Components

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


Mass: 14209.944 Da / Num. of mol.: 2 / Mutation: K93Q, C129S, A155Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Plasmid: pUNDER / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q16552
#2: Antibody scFv CAT2200 LH


Mass: 26616.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUNDER / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 100 mM Tris, 200 mM LiSO4, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016 / Details: mirrors
RadiationMonochromator: ACCEL SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→43.69 Å / Num. obs: 18382 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 3.22 % / Biso Wilson estimate: 47.405 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.08 / Χ2: 0.914 / Net I/σ(I): 13.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.68-2.750.5222.5713410.9230.6291.8
2.75-2.820.2834.0614140.9560.33599.2
2.82-2.910.2384.5813790.970.28198.7
2.91-30.1915.8713240.9780.22799
3-3.090.1846.1513090.9690.22299
3.09-3.20.1338.3312320.9830.15998.9
3.2-3.320.1099.3212030.9910.13198.7
3.32-3.460.09210.397310.9910.11360.6
3.46-3.610.0912.3810070.990.10991.4
3.61-3.790.07214.486870.9930.0964.2
3.79-40.06415.517600.9930.0872.1
4-4.240.0520.469510.9960.0698.3
4.24-4.530.04323.829030.9970.05298.2
4.53-4.890.0425.578270.9960.04898.2
4.89-5.360.0425.097860.9970.04898.5
5.36-5.990.04222.567070.9970.05198.9
5.99-6.920.04122.976320.9960.0598.8
6.92-8.470.03526.565360.9980.04198.5
8.47-11.990.02829.724190.9980.03498.1
11.99-43.690.02429.912340.9990.02995.1

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QHU

4qhu


Resolution: 2.68→43.69 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 854 4.66 %
Rwork0.2209 17489 -
obs0.2231 18343 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.64 Å2 / Biso mean: 48.0345 Å2 / Biso min: 20.66 Å2
Refinement stepCycle: final / Resolution: 2.68→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 20 73 4943
Biso mean--52.04 43.83 -
Num. residues----646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1940X-RAY DIFFRACTION11.964TORSIONAL
12D1940X-RAY DIFFRACTION11.964TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.68-2.850.40551370.3063001313896
2.85-3.070.32351360.25893109324599
3.07-3.380.26841600.24593112327299
3.38-3.860.27261320.24872156228869
3.86-4.870.24021300.18162907303792
4.87-43.690.24181590.20083204336399

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