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- PDB-7kq7: Crystal structure of IL21R in complex with an antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 7kq7
TitleCrystal structure of IL21R in complex with an antibody Fab fragment
Components
  • Antibody heavy chain
  • Antibody light chain
  • Interleukin-21 receptor
KeywordsPROTEIN BINDING/Immune System / cytokine receptor / PROTEIN BINDING / PROTEIN BINDING-Immune System complex
Function / homology
Function and homology information


interleukin-21 receptor activity / Interleukin-21 signaling / natural killer cell activation / cytokine receptor activity / immunoglobulin mediated immune response / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / external side of plasma membrane / membrane / plasma membrane
Similarity search - Function
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-21 receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsMosyak, L. / Svenson, K.
CitationJournal: Mabs / Year: 2021
Title: Combining random mutagenesis, structure-guided design and next-generation sequencing to mitigate polyreactivity of an anti-IL-21R antibody.
Authors: Campbell, S.M. / DeBartolo, J. / Apgar, J.R. / Mosyak, L. / McManus, V. / Beyer, S. / Bennett, E.M. / Lambert, M. / Cunningham, O.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody heavy chain
L: Antibody light chain
B: Interleukin-21 receptor


Theoretical massNumber of molelcules
Total (without water)72,2633
Polymers72,2633
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-31 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.482, 246.501, 55.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Antibody heavy chain


Mass: 23848.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Antibody light chain


Mass: 23777.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Interleukin-21 receptor / IL-21R / Novel interleukin receptor


Mass: 24636.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL21R, NILR, UNQ3121/PRO10273 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9HBE5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10% PEG MME 5000 and 0.1M MES, pH 6.5

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Data collection

DiffractionMean temperature: 230 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 47436 / % possible obs: 87.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 1437

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.6.1_357refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house structure

Resolution: 2.203→42.216 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 2497 5.28 %
Rwork0.2148 44788 -
obs0.2161 47285 87.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.491 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 147.77 Å2 / Biso mean: 67.69 Å2 / Biso min: 21.13 Å2
Baniso -1Baniso -2Baniso -3
1--14.7957 Å2-0 Å20 Å2
2---3.5455 Å20 Å2
3---18.3412 Å2
Refinement stepCycle: final / Resolution: 2.203→42.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 0 149 5111
Biso mean---48.36 -
Num. residues----637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095096
X-RAY DIFFRACTIONf_angle_d1.1916930
X-RAY DIFFRACTIONf_chiral_restr0.087766
X-RAY DIFFRACTIONf_plane_restr0.005889
X-RAY DIFFRACTIONf_dihedral_angle_d15.0241820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2033-2.2820.32451580.2782277255
2.282-2.37340.29421860.2541337267
2.3734-2.48140.32272400.2529393678
2.4814-2.61220.28292540.2477448888
2.6122-2.77580.24772750.2318486496
2.7758-2.99010.26612970.2295501099
2.9901-3.29090.24212920.2223506399
3.2909-3.76690.21742610.2009505998
3.7669-4.74480.19082560.1784508598
4.7448-42.2160.22862780.2025513995

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