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Basic information

Entry
Database: PDB / ID: 3iu3
TitleCrystal structure of the Fab fragment of therapeutic antibody Basiliximab in complex with IL-2Ra (CD25) ectodomain
Components
  • Heavy chain of Fab fragment of Basiliximab
  • Interleukin-2 receptor alpha chain
  • Light chain of Fab fragment of Basiliximab
KeywordsIMMUNE SYSTEM / IL-2Ra / CD25 / Basiliximab / Simulect / therapeutic antibody / Disulfide bond / Glycoprotein / Membrane / Receptor / Sushi / Transmembrane
Function / homology
Function and homology information


regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / activation-induced cell death of T cells / IgD immunoglobulin complex / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / IgM immunoglobulin complex ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / activation-induced cell death of T cells / IgD immunoglobulin complex / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / interleukin-2-mediated signaling pathway / activated T cell proliferation / CD22 mediated BCR regulation / inflammatory response to antigenic stimulus / Fc epsilon receptor (FCERI) signaling / Interleukin-2 signaling / positive regulation of T cell differentiation / Classical antibody-mediated complement activation / Initial triggering of complement / positive regulation of activated T cell proliferation / IgG immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / Interleukin receptor SHC signaling / Notch signaling pathway / negative regulation of T cell proliferation / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / negative regulation of inflammatory response / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / RAF/MAP kinase cascade / blood microparticle / Potential therapeutics for SARS / adaptive immune response / cell surface receptor signaling pathway / immune response / inflammatory response / external side of plasma membrane / apoptotic process / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Rubrerythrin, domain 2 ...Rubrerythrin, domain 2 - #230 / Interleukin-2 receptor alpha / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Rubrerythrin, domain 2 / Single Sheet / Ribbon / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-2 receptor subunit alpha / Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDu, J. / Yang, H. / Wang, J. / Ding, J.
CitationJournal: J.Immunol. / Year: 2010
Title: Structural basis for the blockage of IL-2 signaling by therapeutic antibody basiliximab
Authors: Du, J. / Yang, H. / Zhang, D. / Wang, J. / Guo, H. / Peng, B. / Guo, Y. / Ding, J.
History
DepositionAug 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy chain of Fab fragment of Basiliximab
B: Light chain of Fab fragment of Basiliximab
C: Heavy chain of Fab fragment of Basiliximab
D: Light chain of Fab fragment of Basiliximab
H: Heavy chain of Fab fragment of Basiliximab
L: Light chain of Fab fragment of Basiliximab
I: Interleukin-2 receptor alpha chain
J: Interleukin-2 receptor alpha chain
K: Interleukin-2 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,00612
Polymers214,2479
Non-polymers1,7603
Water0
1
A: Heavy chain of Fab fragment of Basiliximab
B: Light chain of Fab fragment of Basiliximab
K: Interleukin-2 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0024
Polymers71,4163
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-19 kcal/mol
Surface area26430 Å2
MethodPISA
2
C: Heavy chain of Fab fragment of Basiliximab
D: Light chain of Fab fragment of Basiliximab
J: Interleukin-2 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0024
Polymers71,4163
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-20 kcal/mol
Surface area26410 Å2
MethodPISA
3
H: Heavy chain of Fab fragment of Basiliximab
L: Light chain of Fab fragment of Basiliximab
I: Interleukin-2 receptor alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0024
Polymers71,4163
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-16 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.051, 137.051, 459.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody Heavy chain of Fab fragment of Basiliximab


Mass: 23144.826 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli)
#2: Antibody Light chain of Fab fragment of Basiliximab


Mass: 22882.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: P01834*PLUS
#3: Protein Interleukin-2 receptor alpha chain / IL-2 receptor alpha subunit / IL-2-RA / IL2-RA / p55 / TAC antigen


Mass: 25388.348 Da / Num. of mol.: 3
Fragment: Extracellular domain, ectodomain, UNP residues 22-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-2Ra / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High five / References: UniProt: P01589
#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M KCl, 0.05 M HEPES pH 7.5, and 45% pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 15, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 57938 / Num. obs: 56779 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 70.77 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 17
Reflection shellResolution: 2.9→3 Å / Redundancy: 10 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2 / Num. unique all: 5347 / Rsym value: 0.561 / % possible all: 94.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIM

1mim


Resolution: 2.9→47.381 Å / SU ML: 2.24 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 28.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2651 4.95 %RANDOM
Rwork0.2148 ---
all0.2172 57625 --
obs0.2172 53580 92.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.25 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso mean: 87.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.003 Å2-0 Å2-0 Å2
2--4.003 Å20 Å2
3----8.007 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12449 0 117 0 12566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612906
X-RAY DIFFRACTIONf_angle_d1.05417481
X-RAY DIFFRACTIONf_dihedral_angle_d18.3484575
X-RAY DIFFRACTIONf_chiral_restr0.0651909
X-RAY DIFFRACTIONf_plane_restr0.0042217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.9530.3561070.2832171227878
2.953-3.010.361400.282297243782
3.01-3.0710.3451090.2762450255986
3.071-3.1380.3191190.2552548266789
3.138-3.2110.3291320.2632567269991
3.211-3.2910.3021390.2472619275892
3.291-3.380.3161440.2382651279594
3.38-3.4790.2621460.2182691283795
3.479-3.5920.2681250.2172777290296
3.592-3.720.2571170.2112745286296
3.72-3.8690.2651450.2092754289997
3.869-4.0450.2541590.2082756291596
4.045-4.2580.2241600.1882754291496
4.258-4.5240.2371600.1682750291096
4.524-4.8730.1981470.1682729287694
4.873-5.3630.2291570.1722796295396
5.363-6.1380.2531380.2012875301397
6.138-7.7280.2731380.2142963310198
7.728-47.3870.2241690.2183036320595
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)
11.11470.6152-0.2292-0.37330.47570.54170.1099-0.07990.09060.1186-0.1374-0.0854-0.1056-0.0040.03090.4956-0.0427-0.03250.2114-0.04850.365757.053-5.2288-10.7684
21.67211.2903-0.1483-0.30380.09450.3267-0.00180.07220.1473-0.0291-0.1434-0.0798-0.1118-0.02640.10210.41310.03680.04080.2842-0.04630.473355.5485-16.3642-24.8784
30.7247-0.7539-0.2715-0.1746-0.40281.08590.19240.12830.1325-0.0082-0.1645-0.0637-0.1873-0.0396-0.01470.52830.0766-0.03630.25670.01710.420674.8702-8.2292-65.6981
41.2747-0.9348-0.1802-0.0201-0.1880.11750.0025-0.06120.04590.1646-0.1107-0.0388-0.09620.0530.08290.46670.0268-0.05670.3751-0.0290.515576.3936-19.4492-51.699
5-0.12490.09180.63261.02810.10660.8651-0.2039-0.1257-0.0389-0.36830.31620.08760.0182-0.145-0.09970.346-0.13670.07520.5058-0.06860.369733.0265-52.6906-65.8418
6-0.35420.23830.45821.57280.25540.1119-0.1534-0.25490.02070.16220.15480.0769-0.0074-0.0569-0.01140.43640.05060.06850.6101-0.12370.465741.956-45.8305-51.7943
71.1364-0.46210.37360.2247-0.61920.13770.3519-0.02-0.3784-0.2723-0.11560.34470.7109-0.0069-0.24140.9006-0.16570.01180.60580.09140.903237.9445-92.5605-54.8966
8-0.06110.0497-0.41430.39590.20891.2760.14910.07510.01860.2090.08540.0564-0.2035-0.2389-0.20110.59580.34780.0840.56290.00080.582937.30937.0937-55.6371
91.1909-0.04730.46040.05090.28750.05480.0967-0.2770.5107-0.09620.09680.0352-0.179-0.0411-0.17350.6718-0.24510.05930.55960.03590.892494.55069.7223-21.4573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 215
2X-RAY DIFFRACTION2chain BB1 - 208
3X-RAY DIFFRACTION3chain CC1 - 215
4X-RAY DIFFRACTION4chain DD1 - 209
5X-RAY DIFFRACTION5chain HH1 - 215
6X-RAY DIFFRACTION6chain LL1 - 208
7X-RAY DIFFRACTION7chain II1 - 302
8X-RAY DIFFRACTION8chain JJ1 - 302
9X-RAY DIFFRACTION9chain KK1

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