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- PDB-6wgl: Dupilumab fab with Crystal Kappa design complexed with human IL-4... -

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Basic information

Entry
Database: PDB / ID: 6wgl
TitleDupilumab fab with Crystal Kappa design complexed with human IL-4 receptor
Components
  • (Dupilumab Fab ...) x 2
  • Interleukin-4 receptor subunit alpha
KeywordsIMMUNE SYSTEM / Dupilumab / hIL4R
Function / homology
Function and homology information


interleukin-4 receptor activity / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / 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 / production of molecular mediator involved in inflammatory response / negative regulation of T-helper 1 cell differentiation / T-helper 1 cell differentiation / 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 / Immunoglobulins / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-4 receptor subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsDruzina, Z. / Atwell, S. / Pustilnik, A. / Antonysamy, S. / Ho, C. / Lieu, R. / Hendle, J. / Benach, J. / Wang, J.
CitationJournal: Plos One / Year: 2020
Title: Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing.
Authors: Lieu, R. / Antonysamy, S. / Druzina, Z. / Ho, C. / Kang, N.R. / Pustilnik, A. / Wang, J. / Atwell, S.
History
DepositionApr 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 23, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn
Item: _atom_site.auth_seq_id / _citation.country ..._atom_site.auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _struct_conn.ptnr2_auth_seq_id
Revision 2.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dupilumab Fab heavy chain
B: Dupilumab Fab light chain
C: Interleukin-4 receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0216
Polymers73,9513
Non-polymers1,0703
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-35 kcal/mol
Surface area28690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.490, 73.490, 412.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody Dupilumab Fab heavy chain


Mass: 25233.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Dupilumab Fab light chain


Mass: 23809.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Non-polymers , 2 types, 27 molecules C

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


Mass: 24908.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL4R, IL4RA, 582J2.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P24394
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 molecules

#4: 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 genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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: 3.77 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100mM Hepes pH 7.5, 25% PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.82→103.11 Å / Num. obs: 28706 / % possible obs: 99.9 % / Redundancy: 21.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.031 / Rrim(I) all: 0.143 / Net I/σ(I): 18.1 / Num. measured all: 617796 / Scaling rejects: 64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.82-2.9722.81.0559251040600.730.2211.0792.999.9
8.92-103.1118.80.0562055610960.9960.0130.05738.799.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WG8

6wg8


Resolution: 2.82→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.866 / SU B: 19.147 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.537 / ESU R Free: 0.365 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3037 1420 5 %RANDOM
Rwork0.2451 ---
obs0.2481 27133 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 172.46 Å2 / Biso mean: 69.611 Å2 / Biso min: 25.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.82→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4641 0 70 26 4737
Biso mean--102.36 48.25 -
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124838
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.6596613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6925.016614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.12624.348184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98415708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8511517
X-RAY DIFFRACTIONr_chiral_restr0.090.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023622
LS refinement shellResolution: 2.82→2.893 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 96 -
Rwork0.298 1919 -
all-2015 -
obs--99.8 %

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