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- PDB-8z8l: structure of IL-4Ra in complex with an nanobody 4E9 -

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Basic information

Entry
Database: PDB / ID: 8z8l
Titlestructure of IL-4Ra in complex with an nanobody 4E9
Components
  • Interleukin-4 receptor subunit alpha
  • nanobody dAb1
KeywordsCYTOKINE / inflammation / antibody / immune disorder
Function / homology
Function and homology information


interleukin-4 receptor activity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / production of molecular mediator involved in inflammatory response / positive regulation of T-helper 2 cell differentiation / interleukin-4-mediated signaling pathway / positive regulation of mast cell degranulation / positive regulation of macrophage activation / cytokine receptor activity / T-helper 2 cell differentiation ...interleukin-4 receptor activity / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / production of molecular mediator involved in inflammatory response / positive regulation of T-helper 2 cell differentiation / interleukin-4-mediated signaling pathway / positive regulation of mast cell degranulation / positive regulation of macrophage activation / cytokine receptor activity / T-helper 2 cell differentiation / positive regulation of myoblast fusion / positive regulation of immunoglobulin production / defense response to protozoan / immunoglobulin mediated immune response / positive regulation of chemokine production / centriolar satellite / cytokine-mediated signaling pathway / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / receptor complex / immune response / external side of plasma membrane / signal transduction / extracellular region / nucleoplasm / plasma membrane
Similarity search - Function
Interleukin-4 receptor alpha, N-terminal / Interleukin-4 receptor alpha chain, N-terminal / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-4 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 Å
AuthorsSong, G. / Qiu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: structure of IL-4Ra in complex with an nanobody 4E9
Authors: Song, G. / Qiu, W.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Interleukin-4 receptor subunit alpha
A: nanobody dAb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7884
Polymers38,1432
Non-polymers6462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-3 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.936, 142.936, 149.087
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Interleukin-4 receptor subunit alpha / IL-4 receptor subunit alpha / IL-4R subunit alpha / IL-4R-alpha / IL-4RA


Mass: 24622.545 Da / Num. of mol.: 1 / Mutation: C182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4R, IL4RA, 582J2.1 / Production host: Homo sapiens (human) / References: UniProt: P24394
#2: Antibody nanobody dAb1


Mass: 13519.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#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.: 1 / Source method: obtained synthetically / 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
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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 1.4 M Sodium malonate dibasic monohydrate pH 6.0

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.96→95.2 Å / Num. obs: 4534 / % possible obs: 92.1 % / Redundancy: 12.4 % / Biso Wilson estimate: 191.38 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.2
Reflection shellResolution: 3.96→4.21 Å / Num. unique obs: 227 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.96→19.82 Å / SU ML: 0.6218 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.9962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3337 225 5.01 %
Rwork0.3011 4263 -
obs0.3028 4488 86.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 208.29 Å2
Refinement stepCycle: LAST / Resolution: 3.96→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 42 0 2381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322443
X-RAY DIFFRACTIONf_angle_d0.67243341
X-RAY DIFFRACTIONf_chiral_restr0.0573374
X-RAY DIFFRACTIONf_plane_restr0.0058425
X-RAY DIFFRACTIONf_dihedral_angle_d5.4316347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.96-4.980.3514930.38331761X-RAY DIFFRACTION72.06
4.98-19.820.32971320.28092502X-RAY DIFFRACTION99.92
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)
18.438700540981.98259065287-2.811201358660.9265252351781.347283980864.85079508612-1.303246510410.4440673201390.288672897375-1.751619134890.4522251780832.16452210011.04269640868-1.282512239020.7422896960312.26507555648-0.204357776096-0.5378481518521.385093818190.1181706217781.8734916965343.511-35.126-6.051
211.3605413422-5.46926538684-0.9307762965468.08450273407-3.588007757126.299617403860.44672317953-0.116347364904-1.437857140920.1855534707040.496504171801-0.7437463628780.702756928998-0.205263007243-1.05388931791.50805789817-0.218465063545-0.09431350127651.41324776621-0.06344936296551.4299860737752.099-56.62615.581
310.68053478611.41182604312-2.674134877789.111970149333.222841679769.19470738568-0.03619961305571.068832927771.43396798250.279646723365-0.44061034831-0.339919376985-0.09245015347630.3391307195680.6215933815831.55899619114-0.220860448616-0.211094172241.930323777270.3555181852482.1311140579340.37-10.49811.74
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:96 )B1 - 96
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1:115 )A1 - 115
3X-RAY DIFFRACTION3( CHAIN B AND RESID 97:197 )B97 - 197

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