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- PDB-7rew: Crystal Structure of IL-13 in complex with MMAb3 Fab -

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Basic information

Entry
Database: PDB / ID: 7rew
TitleCrystal Structure of IL-13 in complex with MMAb3 Fab
Components
  • IL13
  • anti-cyno interleukin 13 Fab heavy chain
  • anti-cyno interleukin 13 Fab light chain
KeywordsCYTOKINE / alpha-helical bundle / protein-Fab complex
Function / homology
Function and homology information


cytokine receptor binding / immune response / extracellular region
Similarity search - Function
Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Model detailsFc
AuthorsSudom, A. / Min, X.
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Development of a potent high-affinity human therapeutic antibody via novel application of recombination signal sequence-based affinity maturation.
Authors: Kielczewska, A. / D'Angelo, I. / Amador, M.S. / Wang, T. / Sudom, A. / Min, X. / Rathanaswami, P. / Pigott, C. / Foltz, I.N.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-cyno interleukin 13 Fab heavy chain
L: anti-cyno interleukin 13 Fab light chain
A: anti-cyno interleukin 13 Fab heavy chain
B: anti-cyno interleukin 13 Fab light chain
G: IL13
I: IL13


Theoretical massNumber of molelcules
Total (without water)118,2966
Polymers118,2966
Non-polymers00
Water2,360131
1
H: anti-cyno interleukin 13 Fab heavy chain
L: anti-cyno interleukin 13 Fab light chain
I: IL13


Theoretical massNumber of molelcules
Total (without water)59,1483
Polymers59,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: anti-cyno interleukin 13 Fab heavy chain
B: anti-cyno interleukin 13 Fab light chain
G: IL13


Theoretical massNumber of molelcules
Total (without water)59,1483
Polymers59,1483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.790, 74.352, 76.530
Angle α, β, γ (deg.)96.848, 109.890, 112.494
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Antibody anti-cyno interleukin 13 Fab heavy chain


Mass: 24108.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) / Tissue (production host): kidney
#2: Antibody anti-cyno interleukin 13 Fab light chain


Mass: 22737.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293T / Production host: Homo sapiens (human) / Tissue (production host): kidney
#3: Protein IL13


Mass: 12302.288 Da / Num. of mol.: 2 / Fragment: UNP residues 22-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: IL13 / Cell line (production host): 293T / Production host: Homo sapiens (human) / Tissue (production host): kidney / References: UniProt: Q0PW92
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.31 Å3/Da / Density % sol: 46.83 % / Mosaicity: 0.3 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 0.2 M LiSO4, 0.1 M Tris HCl pH 8.5, 25% PEG 5,000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 4, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→68.94 Å / Num. obs: 54189 / % possible obs: 88 % / Redundancy: 2.1 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.044 / Rrim(I) all: 0.068 / Net I/σ(I): 7.2 / Num. measured all: 115864 / Scaling rejects: 418
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.170.381976045980.8320.3510.5192.890.4
8.93-68.940.04816617850.9760.0430.06511.896.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CQI

4cqi


Resolution: 2.1→35.96 Å / SU ML: 0.3344 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 36.4314 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2909 2617 4.83 %
Rwork0.245 51516 -
obs0.2473 54133 87.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7581 0 0 131 7712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317768
X-RAY DIFFRACTIONf_angle_d0.679310576
X-RAY DIFFRACTIONf_chiral_restr0.04381203
X-RAY DIFFRACTIONf_plane_restr0.00481334
X-RAY DIFFRACTIONf_dihedral_angle_d10.0444597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.40671490.3772829X-RAY DIFFRACTION90.74
2.14-2.180.39981600.36432787X-RAY DIFFRACTION90.37
2.18-2.230.39041350.33822730X-RAY DIFFRACTION89.81
2.23-2.280.4231440.34992737X-RAY DIFFRACTION88.95
2.28-2.330.37881490.3232750X-RAY DIFFRACTION88.49
2.33-2.390.38371510.3112667X-RAY DIFFRACTION86.92
2.39-2.450.41661390.29932580X-RAY DIFFRACTION84.49
2.45-2.520.34411320.29032461X-RAY DIFFRACTION80.33
2.52-2.610.37071140.292355X-RAY DIFFRACTION76.16
2.61-2.70.38561310.29352851X-RAY DIFFRACTION92.58
2.7-2.810.39571080.282913X-RAY DIFFRACTION92.7
2.81-2.930.34171360.29152820X-RAY DIFFRACTION91.6
2.93-3.090.37581460.28472780X-RAY DIFFRACTION90.59
3.09-3.280.34131060.26722790X-RAY DIFFRACTION89.22
3.28-3.540.32281350.25142630X-RAY DIFFRACTION85
3.54-3.890.23791630.23332375X-RAY DIFFRACTION78.33
3.89-4.450.24141140.19062961X-RAY DIFFRACTION94.85
4.45-5.610.20321460.17992848X-RAY DIFFRACTION92.61
5.61-35.960.22481590.20112652X-RAY DIFFRACTION86.87

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