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- PDB-8dy5: Crystal Structure of spFv CAT2200 LH in complex with IL-17A -

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Basic information

Entry
Database: PDB / ID: 8dy5
TitleCrystal Structure of spFv CAT2200 LH in complex with IL-17A
Components
  • Interleukin-17A
  • spFv 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 / negative regulation of inflammatory response to wounding / intestinal epithelial structure maintenance / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / negative regulation of inflammatory response to wounding / intestinal epithelial structure maintenance / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / 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 / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune response / protein heterodimerization activity / external side of plasma membrane / innate immune response / 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: 2.2 Å
Model detailsCrystal Structure of spFv GLK1 in LH configuration
AuthorsLuo, J. / Boucher, L.E.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,5627
Polymers81,4624
Non-polymers1003
Water5,152286
1
A: spFv CAT2200 LH
C: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7673
Polymers40,7312
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: spFv CAT2200 LH
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7964
Polymers40,7312
Non-polymers642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.430, 226.380, 75.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-213-

HOH

21D-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 9 or resid 11...
21(chain B and (resid 1 through 9 or resid 11...

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
11ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 91 - 9
12SERSERASNASN(chain A and (resid 1 through 9 or resid 11...AA11 - 3111 - 31
13ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
14ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
15ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
16ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
17ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
18ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
19ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
110ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
21ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 91 - 9
22SERSERASNASN(chain B and (resid 1 through 9 or resid 11...BB11 - 3111 - 31
23TYRTYRTYRTYR(chain B and (resid 1 through 9 or resid 11...BB3232
24ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
25ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
26ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
27ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
28ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
29ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
210ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244

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Components

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Antibody / Protein , 2 types, 4 molecules ABCD

#1: Antibody spFv CAT2200 LH


Mass: 26521.256 Da / Num. of mol.: 2 / Mutation: T28G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-17A / Plasmid: pUNDER / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: 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 (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q16552

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Non-polymers , 4 types, 289 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 400 mM LiSO4, 15.5% 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: Jul 18, 2018 / 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: 2.2→45.26 Å / Num. obs: 36090 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 41.718 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.134 / Χ2: 0.838 / Net I/σ(I): 10.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.261.0121.9826300.7241.12799.5
2.26-2.320.9782.0425870.7591.0999.8
2.32-2.390.8162.4125080.8080.9199.8
2.39-2.460.6712.9224290.8470.7599.7
2.46-2.540.5543.523840.8850.6299.8
2.54-2.630.4214.6622680.9280.4799.5
2.63-2.730.3545.422050.9480.39499.5
2.73-2.840.2836.621380.9570.31599.9
2.84-2.970.2138.2220490.9790.23899.9
2.97-3.110.179.9719550.9860.1999.7
3.11-3.280.12712.0218780.9910.14399.7
3.28-3.480.09315.4717520.9950.10499.3
3.48-3.720.07718.6716610.9960.08699.5
3.72-4.020.06620.6715540.9970.07399.4
4.02-4.40.05523.7914350.9970.06199.2
4.4-4.920.04625.6613030.9980.05298.9
4.92-5.680.04624.5811490.9980.05298.6
5.68-6.960.0522.849770.9980.05697.3
6.96-9.840.0427.067760.9990.04598.4
9.84-45.260.03230.334520.9990.03795

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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: 2.2→45.25 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1803 5 %
Rwork0.1879 34266 -
obs0.1902 36069 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.3 Å2 / Biso mean: 42.8986 Å2 / Biso min: 21.14 Å2
Refinement stepCycle: final / Resolution: 2.2→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 3 286 5310
Biso mean--61.94 42.84 -
Num. residues----691
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16X-RAY DIFFRACTION41.058TORSIONAL
12B16X-RAY DIFFRACTION41.058TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.30931360.25772599273599
2.26-2.330.35641390.256426372776100
2.33-2.40.33961350.247225702705100
2.4-2.490.28411380.238226222760100
2.49-2.590.29041390.22226322771100
2.59-2.70.26761370.19812600273799
2.7-2.850.28311380.194326262764100
2.85-3.020.24671390.180226312770100
3.03-3.260.22611380.186626332771100
3.26-3.590.2221400.16172656279699
3.59-4.10.17881390.16512638277799
4.1-5.170.18071400.15482671281199
5.17-45.250.23931450.20582751289698

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