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- PDB-8k4q: Crystal structure of nanobody HuNb103 bound to human interleukin-... -

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Basic information

Entry
Database: PDB / ID: 8k4q
TitleCrystal structure of nanobody HuNb103 bound to human interleukin-4 receptor subunit alpha
Components
  • IL-4R nanobody HuNb103
  • Interleukin-4 receptor subunit alpha
KeywordsCYTOKINE / antibody / complex / IL-4R / IL-4 / IL-13
Function / homology
Function and homology information


production of molecular mediator involved in inflammatory response / cytokine receptor activity / external side of 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)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDing, Y. / Zhong, P.Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070939 China
National Science Foundation (NSF, China)82030106 China
Ministry of Science and Technology (MoST, China)2021YFA0805200 China
CitationJournal: J.Allergy Clin.Immunol. / Year: 2024
Title: A Novel Inhalable Nanobody Targeting IL-4R alpha for the Treatment of Asthma.
Authors: Zhu, M. / Ma, L. / Zhong, P. / Huang, J. / Gai, J. / Li, G. / Li, Y. / Qiao, P. / Gu, H. / Li, X. / Yin, Y. / Zhang, L. / Deng, Z. / Sun, B. / Chen, Z. / Ding, Y. / Wan, Y.
History
DepositionJul 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-4 receptor subunit alpha
B: IL-4R nanobody HuNb103
C: Interleukin-4 receptor subunit alpha
D: IL-4R nanobody HuNb103
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,23312
Polymers75,3264
Non-polymers2,9078
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, isothermal titration calorimetry, mass spectrometry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.870, 109.598, 64.167
Angle α, β, γ (deg.)90.00, 98.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody / Non-polymers , 3 types, 141 molecules ACBD

#1: Protein Interleukin-4 receptor subunit alpha


Mass: 24606.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q53EP8
#2: Antibody IL-4R nanobody HuNb103


Mass: 13056.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 8 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.: 2 / Source method: isolated from a natural 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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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: 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

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Details

Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir condition: 0.1M HEPES pH 7.0, 20% PEG8000. Sample buffer: 25mM HEPES pH 7.49, 150mM NaCl. Cryoprotectant condition: 0.1M HEPES pH 7.0, 20% PEG8000, 15% ethylene glycol.
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.59→109.6 Å / Num. obs: 24709 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.066 / Rrim(I) all: 0.169 / Χ2: 0.81 / Net I/σ(I): 9.7 / Num. measured all: 161738
Reflection shellResolution: 2.59→2.66 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 2.158 / Num. measured all: 11813 / Num. unique obs: 1843 / CC1/2: 0.412 / Rpim(I) all: 0.925 / Rrim(I) all: 2.351 / Χ2: 0.51 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALSdata scaling
DIALSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→57.3 Å / SU B: 32.922 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 0.896 / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27987 1186 4.8 %RANDOM
Rwork0.22211 ---
obs0.2249 23495 99.96 %-
Displacement parametersBiso mean: 31.526 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å2-0 Å21.35 Å2
2---4.38 Å2-0 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.59→57.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 190 137 5308
LS refinement shellHighest resolution: 2.59 Å
RfactorNum. reflection% reflection
Rfree0.3574 --
Rwork0.3621 --
obs-2444 99.8 %

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