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- PDB-5hhv: Inhibiting complex IL-17A and IL-17RA interactions with a linear ... -

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Basic information

Entry
Database: PDB / ID: 5hhv
TitleInhibiting complex IL-17A and IL-17RA interactions with a linear peptide
Components
  • CAT-2000 FAB heavy chain
  • CAT-2000 FAB light chain
  • IL-17A peptide inhibitor
  • Interleukin-17A
KeywordsIMMUNE SYSTEM/INHIBITOR / IL-17 / inflammation / inhibitor / complex crystal structure / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death / 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 / defense response to fungus / cellular response to interleukin-1 / 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 / immune response / inflammatory 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, S.
CitationJournal: Sci Rep / Year: 2016
Title: Inhibiting complex IL-17A and IL-17RA interactions with a linear peptide.
Authors: Liu, S. / Desharnais, J. / Sahasrabudhe, P.V. / Jin, P. / Li, W. / Oates, B.D. / Shanker, S. / Banker, M.E. / Chrunyk, B.A. / Song, X. / Feng, X. / Griffor, M. / Jimenez, J. / Chen, G. / ...Authors: Liu, S. / Desharnais, J. / Sahasrabudhe, P.V. / Jin, P. / Li, W. / Oates, B.D. / Shanker, S. / Banker, M.E. / Chrunyk, B.A. / Song, X. / Feng, X. / Griffor, M. / Jimenez, J. / Chen, G. / Tumelty, D. / Bhat, A. / Bradshaw, C.W. / Woodnutt, G. / Lappe, R.W. / Thorarensen, A. / Qiu, X. / Withka, J.M. / Wood, L.D.
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-17A
B: Interleukin-17A
H: CAT-2000 FAB heavy chain
I: IL-17A peptide inhibitor
L: CAT-2000 FAB light chain


Theoretical massNumber of molelcules
Total (without water)78,3815
Polymers78,3815
Non-polymers00
Water91951
1
A: Interleukin-17A
B: Interleukin-17A
H: CAT-2000 FAB heavy chain
I: IL-17A peptide inhibitor
L: CAT-2000 FAB light chain

A: Interleukin-17A
B: Interleukin-17A
H: CAT-2000 FAB heavy chain
I: IL-17A peptide inhibitor
L: CAT-2000 FAB light chain


Theoretical massNumber of molelcules
Total (without water)156,76310
Polymers156,76310
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_647y+1,x-1,-z+21
Unit cell
Length a, b, c (Å)110.200, 110.200, 90.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11H-331-

HOH

21H-332-

HOH

31H-333-

HOH

DetailsThe biological assemble of the complex consists two IL-17A monomer forming a dimer, two Fab binding to IL-17A dimer and two peptide interacting with IL-17A

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Components

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


Mass: 14235.937 Da / Num. of mol.: 2 / Fragment: UNP residues 34-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16552
#2: Antibody CAT-2000 FAB heavy chain


Mass: 25053.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide IL-17A peptide inhibitor


Mass: 1849.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Antibody CAT-2000 FAB light chain


Mass: 23006.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: .02 mM CdCl2, 0.02 M MgCl2, 0.02 M NiCl2, 0.1 M NaOAc pH=4.2-4.9, and 24-28 % PEG MME 2000
PH range: 4.2-4.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→95.43 Å / Num. obs: 32509 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 56.29 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.46 Å / Redundancy: 8 % / Rmerge(I) obs: 0.149 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
autoPROCdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VXS

2vxs


Resolution: 2.2→95.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1674 5.17 %RANDOM
Rwork0.198 ---
obs0.1999 32381 99.48 %-
Displacement parametersBiso mean: 67.38 Å2
Baniso -1Baniso -2Baniso -3
1--5.1587 Å20 Å20 Å2
2---5.1587 Å20 Å2
3---10.3174 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.2→95.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 0 51 4239
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014302HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.195878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1393SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes629HARMONIC5
X-RAY DIFFRACTIONt_it4302HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion20.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion571SEMIHARMONIC5
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_contact4610SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.27 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2785 143 5.09 %
Rwork0.2395 2666 -
all0.2414 2809 -
obs--99.48 %
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)
11.9640.31761.17921.6131-0.01111.05390.22070.0302-0.3829-0.1961-0.1534-0.05390.27280.1272-0.0673-0.02910.1252-0.0151-0.02290.035-0.114590.0432-49.996188.5742
20.6001-0.284-0.08410.3387-0.05111.8683-0.0066-0.05910.06940.10940.02590.0287-0.00960.0274-0.0193-0.05160.0030.0005-0.0498-0.0052-0.0464104.9087-46.9616127.079
31.0778-0.35951.31860.9212-1.7527.5346-0.20520.13140.42450.3188-0.23-0.2122-1.19451.19270.43520.0482-0.1699-0.07370.0532-0.01910.0603113.593-31.0938129.275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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