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- PDB-4hwe: Crystal structure of ectodomain 3 of the IL-13 receptor alpha1 in... -

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Basic information

Entry
Database: PDB / ID: 4hwe
TitleCrystal structure of ectodomain 3 of the IL-13 receptor alpha1 in complex with a human neutralizing monoclonal antibody fragment
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / Fab / FNIII
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsXu, Y.
CitationJournal: Biochem.J. / Year: 2013
Title: Crystal structure of ectodomain 3 of the IL-13 receptor alpha1 in complex with a human neutralizing monoclonal antibody fragment
Authors: Redpath, N.T. / Xu, Y. / Wilson, N.J. / Fabri, L.J. / Baca, M. / Andrews, A.E. / Braley, H. / Lu, P. / Ireland, C. / Ernst, R.E. / Woods, A. / Forrest, G. / An, Z. / Zaller, D.M. / Strohl, W. ...Authors: Redpath, N.T. / Xu, Y. / Wilson, N.J. / Fabri, L.J. / Baca, M. / Andrews, A.E. / Braley, H. / Lu, P. / Ireland, C. / Ernst, R.E. / Woods, A. / Forrest, G. / An, Z. / Zaller, D.M. / Strohl, W.R. / Luo, C.S. / Czabotar, P.E. / Garrett, T.P. / Hilton, D.J. / Nash, A.D. / Zhang, J.G. / Nicola, N.A.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,70916
Polymers47,4042
Non-polymers1,30514
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-58 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.364, 121.364, 152.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Antibody Fab heavy chain


Mass: 24342.398 Da / Num. of mol.: 1 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab light chain


Mass: 23061.533 Da / Num. of mol.: 1 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.2 M (NH4)2SO4, 0.5% PEG8000, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. all: 21666 / Num. obs: 21620 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 50.46 Å2
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 7 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→42.91 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9156 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1107 5.12 %RANDOM
Rwork0.1753 ---
obs0.1778 21607 99.38 %-
Displacement parametersBiso mean: 40.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.7733 Å20 Å20 Å2
2--2.7733 Å20 Å2
3----5.5465 Å2
Refine analyzeLuzzati coordinate error obs: 0.267 Å
Refinement stepCycle: LAST / Resolution: 2.43→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 80 243 3531
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013359HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.254559HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1092SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it3359HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion18.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion433SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3759SEMIHARMONIC4
LS refinement shellResolution: 2.43→2.55 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2355 139 5.03 %
Rwork0.1788 2622 -
all0.1817 2761 -
obs--99.38 %
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)
11.0839-0.04860.01631.6862-0.03330.62660.0227-0.06860.0801-0.06040.0074-0.03550.0525-0.0406-0.0301-0.0476-0.00110.0156-0.04490.01710.021515.522421.05927.5954
21.6077-0.720.39263.8973-0.7011.8878-0.0776-0.16410.2998-0.19730.0506-0.3052-0.5309-0.03880.02690.02780.0213-0.0156-0.1256-0.0092-0.052319.288156.241630.0847
31.61670.03020.27093.576-1.0271.240.01950.06030.1256-0.3071-0.00170.1429-0.0258-0.0375-0.0177-0.0214-0.0106-0.0286-0.06120.0095-0.054-1.552229.443615.2018
42.86650.02430.16993.3954-0.10281.51640.06410.28140.1955-0.4866-0.1392-0.2238-0.20460.19990.07510.090.01540.0448-0.1640.0653-0.148118.526858.80813.891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|2 - H|119 }H2 - 119
2X-RAY DIFFRACTION2{ H|120 - H|220 }H120 - 220
3X-RAY DIFFRACTION3{ L|1 - L|104 }L1 - 104
4X-RAY DIFFRACTION4{ L|105 - L|210 }L105 - 210

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