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- PDB-9eza: Interleukin-31 Receptor D1D2 in complex with Nemolizumab derived scFv -

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Basic information

Entry
Database: PDB / ID: 9eza
TitleInterleukin-31 Receptor D1D2 in complex with Nemolizumab derived scFv
Components
  • Interleukin-31 receptor subunit alpha
  • Nemolizumab scFv
KeywordsCYTOKINE / cytokine receptor / complex / antibody / antagonist
Function / homology
Function and homology information


negative regulation of macrophage activation / glandular epithelial cell differentiation / defense response to other organism / acute inflammatory response to antigenic stimulus / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / positive regulation of tyrosine phosphorylation of STAT protein / homeostatic process / cytokine binding / monocyte differentiation ...negative regulation of macrophage activation / glandular epithelial cell differentiation / defense response to other organism / acute inflammatory response to antigenic stimulus / IL-6-type cytokine receptor ligand interactions / cytokine receptor activity / positive regulation of tyrosine phosphorylation of STAT protein / homeostatic process / cytokine binding / monocyte differentiation / macrophage differentiation / cell surface receptor signaling pathway via JAK-STAT / cell surface receptor protein tyrosine kinase signaling pathway / defense response / cytokine-mediated signaling pathway / MAPK cascade / presynaptic membrane / transcription coactivator activity / receptor complex / external side of plasma membrane / axon / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / membrane / plasma membrane
Similarity search - Function
: / Type I cytokine receptor, cytokine-binding domain / Interleukin-6 receptor alpha chain, binding / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Interleukin-31 receptor subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.147 Å
AuthorsBloch, Y. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)12S0519N Belgium
CitationJournal: To Be Published
Title: Structural basis of the Interleukin-31 signaling complex and its inhibition.
Authors: Bloch, Y. / Savvides, S.N.
History
DepositionApr 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nemolizumab scFv
B: Interleukin-31 receptor subunit alpha
C: Nemolizumab scFv
D: Interleukin-31 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,37510
Polymers115,8534
Non-polymers1,5226
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-7 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.008, 163.559, 269.466
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Antibody / Protein , 2 types, 4 molecules ACBD

#1: Antibody Nemolizumab scFv


Mass: 27660.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: humanized / Source: (gene. exp.) Mus musculus (house mouse) / Cell line: hybridoma / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express
#2: Protein Interleukin-31 receptor subunit alpha / IL-31 receptor subunit alpha / IL-31R subunit alpha / IL-31R-alpha / IL-31RA / Cytokine receptor- ...IL-31 receptor subunit alpha / IL-31R subunit alpha / IL-31R-alpha / IL-31RA / Cytokine receptor-like 3 / GLM-R / hGLM-R / Gp130-like monocyte receptor / Gp130-like receptor / ZcytoR17


Mass: 30266.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: [1-18] Expected secretion signal [19-223] Protein [224-225] Restricition site [227-230] Caspase3 protease site [231-261] Avi His tag
Source: (gene. exp.) Homo sapiens (human) / Gene: IL31RA, CRL3, GPL, UNQ6368/PRO21073/PRO21384 / Plasmid: pHLsec / Cell line (production host): HEK293S MGat -/- / Production host: Homo sapiens (human) / References: UniProt: Q8NI17

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Sugars , 2 types, 5 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 243 molecules

#5: Chemical ChemComp-A1H79 / BES buffer / 2-[bis(2-hydroxyethyl)amino]ethanesulfonic acid


Mass: 213.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: MorpheusII H6 (40 mM Polyamines, 10% PEG4000, 20% 1,2,6-Hexanetriol, 100 mM BES pH 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.147→78.378 Å / Num. obs: 70477 / % possible obs: 99.8 % / Redundancy: 6.73 % / Biso Wilson estimate: 56.558 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.112 / Net I/σ(I): 10.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
6.42-78.3786.1933.728560.9980.05199.7
2.28-2.437.131.46106230.6311.144100
2.147-2.285.980.71111480.3021.88198.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDS20180808data reduction
XDS20180808data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.147→46.745 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.311 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.187 / ESU R Free: 0.163
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2303 1995 2.841 %
Rwork0.2009 68228 -
all0.202 --
obs-70223 99.541 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 66.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.284 Å20 Å2-0 Å2
2--0.197 Å20 Å2
3----0.482 Å2
Refinement stepCycle: LAST / Resolution: 2.147→46.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6901 0 69 242 7212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166463
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.8229733
X-RAY DIFFRACTIONr_angle_other_deg0.5171.75914974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.589534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.236101160
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.4910312
X-RAY DIFFRACTIONr_chiral_restr0.0670.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021649
X-RAY DIFFRACTIONr_nbd_refined0.1960.21088
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.25757
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23425
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.23657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2305
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.27
X-RAY DIFFRACTIONr_nbd_other0.1580.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.210
X-RAY DIFFRACTIONr_mcbond_it2.7133.7653501
X-RAY DIFFRACTIONr_mcbond_other2.7133.7653501
X-RAY DIFFRACTIONr_mcangle_it4.0676.7494364
X-RAY DIFFRACTIONr_mcangle_other4.0676.7494365
X-RAY DIFFRACTIONr_scbond_it3.7454.1743660
X-RAY DIFFRACTIONr_scbond_other3.7454.1763661
X-RAY DIFFRACTIONr_scangle_it5.7867.5055369
X-RAY DIFFRACTIONr_scangle_other5.7867.5065370
X-RAY DIFFRACTIONr_lrange_it7.80135.9167574
X-RAY DIFFRACTIONr_lrange_other7.80135.9247575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.147-2.2030.4391380.40746920.40851320.8690.89294.11540.41
2.203-2.2630.3461420.36948730.36850170.9030.90599.96010.37
2.263-2.3290.3181390.3347700.3349090.9190.9311000.326
2.329-2.40.2761350.29746170.29647520.9530.9471000.285
2.4-2.4790.2721300.26944600.26945900.9520.961000.25
2.479-2.5650.3241270.23643100.23944380.9480.96999.97750.213
2.565-2.6620.2371230.20941890.2143120.9680.9751000.184
2.662-2.770.2921170.19740540.241710.9570.9771000.173
2.77-2.8930.2471140.19138790.19339950.960.97999.94990.17
2.893-3.0330.2211070.18836900.18937970.9730.9821000.169
3.033-3.1970.2471040.21235200.21336240.9650.9761000.198
3.197-3.390.265980.21833510.21934490.960.9761000.207
3.39-3.6220.246930.21631970.21732900.9660.9791000.21
3.622-3.9110.21860.19629220.19630080.9760.981000.193
3.911-4.2810.184790.16327230.16428020.9770.9851000.166
4.281-4.7810.141730.13424850.13425580.9890.991000.143
4.781-5.5110.173640.15221960.15322600.9840.9891000.164
5.511-6.7270.237560.20418930.20519500.9750.98199.94870.215
6.727-9.4160.208430.18414980.18515420.9780.98199.93520.205
9.416-46.7450.316270.2189090.229410.8910.96799.46870.242
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)
11.2466-0.3745-0.03222.4587-1.40721.59370.0673-0.08760.1498-0.2355-0.2209-0.12440.0760.35070.15360.08550.00610.04170.0940.06510.2225-18.181854.078940.4068
22.57010.41580.2921.6256-0.19251.57520.0294-0.1465-0.03190.0283-0.08010.0530.23220.0660.05070.1151-0.00440.05120.0180.00540.130221.455933.247757.4743
31.68840.6127-0.48313.6088-0.60142.6627-0.0477-0.02810.0755-0.2847-0.0604-0.4-0.05950.55390.10810.3244-0.01980.05470.27590.1560.3087-6.43874.41118.6038
41.659-0.07290.36011.92361.09563.7309-0.13120.4957-0.3054-0.6859-0.04230.31580.8583-0.55230.17351.1288-0.2508-0.03090.39180.04470.3977-26.13653.1398-0.1443
51.6652-0.64340.17641.5626-0.63061.14960.05220.05660.1807-0.11170.04240.26260.0836-0.2136-0.09460.0775-0.0380.01940.06270.01410.30134.419643.729946.4239
62.10930.4969-0.64982.2714-0.76051.69270.127-0.01330.46810.04270.00680.4098-0.3234-0.0411-0.13380.15980.00460.02180.0030.0140.4143-34.902769.825840.3437
71.4397-0.4474-0.16812.7268-0.33462.8955-0.05840.0242-0.160.08820.06020.71270.3798-0.5812-0.00180.3591-0.21210.02450.2492-0.01680.5396-6.501115.500847.0117
80.5509-0.516-1.0621.50310.29964.10940.10180.07010.0971-0.26-0.14590.03130.02640.02230.04420.4163-0.1078-0.06940.16320.03280.2969.867213.000323.8268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp1 - 137
2X-RAY DIFFRACTION2ALLAp138 - 243

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