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- PDB-6h41: Structure of the complex of the IL-5 inhibitory peptide AF17121 b... -

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Basic information

Entry
Database: PDB / ID: 6h41
TitleStructure of the complex of the IL-5 inhibitory peptide AF17121 bound to the IL-5 receptor IL-5Ralpha
Components
  • Interleukin-5 receptor subunit alpha
  • VAL-ASP-GLU-CYS-TRP-ARG-ILE-ILE-ALA-SER-HIS-THR-TRP-PHE-CYS-ALA-GLU-GLU
KeywordsCYTOKINE / Interleukin-5 / inhibitor peptide / peptide-receptor complex / atopic diseases
Function / homology
Function and homology information


interleukin-5 receptor activity / regulation of interleukin-5 production / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / inflammatory response to antigenic stimulus / cytokine receptor activity / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cytokine-mediated signaling pathway ...interleukin-5 receptor activity / regulation of interleukin-5 production / interleukin-5-mediated signaling pathway / positive regulation of leukocyte proliferation / inflammatory response to antigenic stimulus / cytokine receptor activity / cytokine binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / cytokine-mediated signaling pathway / RAF/MAP kinase cascade / receptor complex / external side of plasma membrane / signal transduction / extracellular space / membrane / plasma membrane
Similarity search - Function
Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Short hematopoietin receptor, family 2, conserved site / Short hematopoietin receptor family 2 signature. / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-5 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsMueller, T.D. / Scheide, J.P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationMU1095/7-1 Germany
Citation
Journal: J. Mol. Biol. / Year: 2019
Title: Structural Basis of Interleukin-5 Inhibition by the Small Cyclic Peptide AF17121.
Authors: Scheide-Noeth, J.P. / Rosen, M. / Baumstark, D. / Dietz, H. / Mueller, T.D.
#1: Journal: Structure / Year: 2011
Title: Structure analysis of the IL-5 ligand-receptor complex reveals a wrench-like architecture for IL-5Ralpha.
Authors: Patino, E. / Kotzsch, A. / Saremba, S. / Nickel, J. / Schmitz, W. / Sebald, W. / Mueller, T.D.
History
DepositionJul 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-5 receptor subunit alpha
B: VAL-ASP-GLU-CYS-TRP-ARG-ILE-ILE-ALA-SER-HIS-THR-TRP-PHE-CYS-ALA-GLU-GLU


Theoretical massNumber of molelcules
Total (without water)37,3902
Polymers37,3902
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-8 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.061, 138.061, 145.855
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Interleukin-5 receptor subunit alpha / / IL-5RA / CDw125


Mass: 35192.633 Da / Num. of mol.: 1 / Mutation: C66A
Source method: isolated from a genetically manipulated source
Details: extracellullar domain of the human interleukin-5 receptor subunit alpha (Uniprot: Q01344-2), cysteine 66 is replaced with alanine
Source: (gene. exp.) Homo sapiens (human) / Gene: IL5RA, IL5R / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta(DE3) / References: UniProt: Q01344
#2: Protein/peptide VAL-ASP-GLU-CYS-TRP-ARG-ILE-ILE-ALA-SER-HIS-THR-TRP-PHE-CYS-ALA-GLU-GLU


Mass: 2197.448 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: monomeric cyclic IL-5 inhibiting peptide AF17121, disulfide-bridge between Cys4 and Cys15
Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate pH 5.0, 3% (w/v) PEG 4000, 15% - 20% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.728→119.564 Å / Num. all: 21928 / Num. obs: 21928 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 87.67 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.145 / Rsym value: 0.139 / Net I/av σ(I): 1.9 / Net I/σ(I): 13.3 / Num. measured all: 322542
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.75-2.915.62.8040.24845031040.7312.8992.8042.3100
2.9-3.0715.41.4310.44585729750.3741.481.4313.8100
3.07-3.2914.30.5941.14002628000.1610.6160.5946.4100
3.29-3.5514.50.2682.53796426130.0720.2780.26810.7100
3.55-3.8915.40.1654.13720324220.0430.1710.16514.7100
3.89-4.3514.20.1125.73127322060.0310.1170.11218.8100
4.35-5.0214.90.0897.32939219680.0240.0920.08924.6100
5.02-6.1514.50.0887.12442616840.0240.0910.08825.2100
6.15-8.713.60.0886.81836913500.0240.0910.08826100
8.7-43.16711.90.0823.895828060.0280.0870.08229.299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→43.167 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 2096 5.19 %
Rwork0.2024 38279 -
obs0.2036 40375 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 257.87 Å2 / Biso mean: 106.1047 Å2 / Biso min: 60.03 Å2
Refinement stepCycle: final / Resolution: 2.75→43.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 24 2661
Biso mean---91.31 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032711
X-RAY DIFFRACTIONf_angle_d0.9093692
X-RAY DIFFRACTIONf_chiral_restr0.032408
X-RAY DIFFRACTIONf_plane_restr0.003472
X-RAY DIFFRACTIONf_dihedral_angle_d13.433974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.75-2.8140.36031340.339625442678
2.814-2.88430.33741300.32525332663
2.8843-2.96230.34681260.294625542680
2.9623-3.04940.3141550.295125562711
3.0494-3.14780.28351460.262425502696
3.1478-3.26030.24381320.265525502682
3.2603-3.39080.34761670.254825272694
3.3908-3.54510.26881230.237425862709
3.5451-3.73190.23691280.228625632691
3.7319-3.96550.27751330.22325352668
3.9655-4.27150.27451380.200825762714
4.2715-4.70080.19631550.165725282683
4.7008-5.380.18681640.1625462710
5.38-6.7740.18161460.186125412687
6.774-43.17190.1681190.171625902709
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)
11.4066-0.3291-1.17330.99990.23113.01770.32770.2344-0.1236-0.1783-0.02420.20770.1343-0.51110.00460.87440.06110.050.64320.13880.816354.9456-17.1263-9.9587
20.19210.02050.11740.06070.1170.34950.25670.43970.937-0.61330.08110.7225-1.25430.00030.00711.5627-0.07350.35610.75210.24531.188350.7346-6.88940.4999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 315)A7 - 315
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 18)B1 - 18

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