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

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Basic information

Entry
Database: PDB / ID: 5hhx
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 / 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 / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / gene expression / 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: 3 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)81,4515
Polymers81,4515
Non-polymers00
Water543
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)162,90210
Polymers162,90210
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_647y+1,x-1,-z+21
Unit cell
Length a, b, c (Å)113.400, 113.400, 86.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 15770.871 Da / Num. of mol.: 2 / Fragment: UNP residues 20-155
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


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M NaOAc, pH=4.5 and 30% PEG MME 5000 / PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→25.23 Å / Num. obs: 13244 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 101.16 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.4
Reflection shellResolution: 3→3.35 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.15 / % 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: 3→25.23 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.8821 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.431
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 647 4.91 %RANDOM
Rwork0.1763 ---
obs0.1802 13170 99.63 %-
Displacement parametersBiso mean: 112.32 Å2
Baniso -1Baniso -2Baniso -3
1--15.2345 Å20 Å20 Å2
2---15.2345 Å20 Å2
3---30.4689 Å2
Refine analyzeLuzzati coordinate error obs: 0.523 Å
Refinement stepCycle: 1 / Resolution: 3→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 0 3 4123
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014225HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.295765HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1373SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes614HARMONIC5
X-RAY DIFFRACTIONt_it4225HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion23.03
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_contact4591SEMIHARMONIC4
LS refinement shellResolution: 3→3.24 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3023 125 4.72 %
Rwork0.2249 2524 -
all0.2285 2649 -
obs--99.63 %
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)
13.16620.97262.18212.14220.66093.8678-0.09770.4447-0.1373-0.1165-0.4214-0.4802-0.40570.36380.51910.33750.26890.0340.65430.09330.264892.8388-48.150884.8891
22.1474-0.03751.40351.10280.14475.2473-0.2533-0.26870.38550.25070.06120.0422-0.1871-0.43320.19210.23810.0433-0.0290.2443-0.06480.298106.7175-48.3804123.463
32.36360.49681.80332.38990.91946.9642-0.6076-0.02760.86780.0640.0972-0.1098-1.42790.53790.51040.2507-0.0764-0.19970.1137-0.13990.5282114.9206-32.3794126.266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ H|* }
3X-RAY DIFFRACTION3{ L|* }

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