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- PDB-4yue: Mouse IL-2 Bound to S4B6 Fab Fragment -

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Basic information

Entry
Database: PDB / ID: 4yue
TitleMouse IL-2 Bound to S4B6 Fab Fragment
Components
  • Interleukin-2
  • S4B6 Fab heavy chain
  • S4B6 Fab light chain
KeywordsCYTOKINE/IMMUNE SYSTEM / chemokine / antibody / complex / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / leukocyte activation involved in immune response ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / tyrosine phosphorylation of STAT protein / positive regulation of regulatory T cell differentiation / : / negative regulation of B cell apoptotic process / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / gene expression / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle ...Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.194 Å
AuthorsSpangler, J.B. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI51321 United States
CitationJournal: Immunity / Year: 2015
Title: Antibodies to Interleukin-2 Elicit Selective T Cell Subset Potentiation through Distinct Conformational Mechanisms.
Authors: Spangler, J.B. / Tomala, J. / Luca, V.C. / Jude, K.M. / Dong, S. / Ring, A.M. / Votavova, P. / Pepper, M. / Kovar, M. / Garcia, K.C.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Source and taxonomy
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: S4B6 Fab heavy chain
L: S4B6 Fab light chain
C: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5704
Polymers65,4783
Non-polymers921
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-26 kcal/mol
Surface area24360 Å2
Unit cell
Length a, b, c (Å)43.080, 77.560, 169.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody S4B6 Fab heavy chain


Mass: 25794.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody S4B6 Fab light chain


Mass: 24727.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#3: Protein Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 14956.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il2, Il-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04351
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Bis-Tris propane, pH 6.5, 0.2 M sodium fluoride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.19→57.2 Å / Num. obs: 29462 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 43.93 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.116 / Χ2: 0.957 / Net I/σ(I): 12.11 / Num. measured all: 192408
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.19-2.330.5351.3061.4729947475246091.42197
2.33-2.490.7650.8712.3129394446144190.94699.1
2.49-2.690.9240.508427029421441680.55398.9
2.69-2.940.9690.2787.1225388381337730.30299
2.94-3.290.9910.14312.5922421352434890.15599
3.29-3.80.9970.07521.2820527310230690.08198.9
3.8-4.650.9980.04629.3917017267426390.0598.7
4.65-6.560.9980.04432.1213233210620660.04898.1
6.560.9970.04935.167451125312290.05498.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
XDS20140110data reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
XDS20140110data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B5I

2b5i


Resolution: 2.194→57.146 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1475 5.01 %
Rwork0.2031 --
obs0.2046 29457 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→57.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 6 223 4420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074327
X-RAY DIFFRACTIONf_angle_d1.1985895
X-RAY DIFFRACTIONf_dihedral_angle_d14.2981580
X-RAY DIFFRACTIONf_chiral_restr0.054683
X-RAY DIFFRACTIONf_plane_restr0.008748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1943-2.26510.34761290.32822440X-RAY DIFFRACTION95
2.2651-2.34610.33721310.29312482X-RAY DIFFRACTION99
2.3461-2.440.31851320.282511X-RAY DIFFRACTION99
2.44-2.55110.30461340.27012524X-RAY DIFFRACTION99
2.5511-2.68560.28871330.23672547X-RAY DIFFRACTION99
2.6856-2.85380.27421330.24172507X-RAY DIFFRACTION99
2.8538-3.07420.26861340.23752535X-RAY DIFFRACTION99
3.0742-3.38350.25051350.20782557X-RAY DIFFRACTION99
3.3835-3.8730.20441360.18332578X-RAY DIFFRACTION99
3.873-4.87920.1631360.15362592X-RAY DIFFRACTION99
4.8792-57.1650.21191420.17882709X-RAY DIFFRACTION98
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)
18.1294-3.9185-4.48014.41374.37554.7283-0.6122-1.6005-0.72911.2568-0.2862-2.10071.31650.94930.76790.82130.19760.10351.07450.36470.8403-8.254-43.95544.7136
25.3717-5.0457-3.90115.33524.24843.4404-0.5302-1.18641.92163.15871.4403-1.8417-0.1001-0.6021-1.10191.05460.3898-0.15411.2304-0.12440.8741-12.4766-29.895650.8837
37.8376-2.782-0.50558.9161.6488.5025-0.0396-0.8885-0.81990.7735-0.04730.25350.2866-0.63880.08810.52680.00280.0570.70650.14130.3964-18.0643-34.843135.468
45.8786-3.1764-4.11636.1749-2.43237.96960.0952-1.50611.41280.70840.6163-1.7093-0.53550.1176-0.30760.5278-0.0261-0.08511.0211-0.1370.649-8.7827-25.530541.1047
58.60091.61250.59966.8524-1.46060.4163-1.17020.5712-0.5035-0.58650.9493-0.21670.81060.5774-0.12910.9362-0.0446-0.0491.4987-0.27310.7056-0.9459-28.84444.3611
65.7146-1.6075-1.95758.68276.22824.5935-0.6771-0.7727-0.79420.92881.1235-0.03360.47730.4604-0.50020.61460.19250.02350.83030.21520.4656-4.7847-39.142536.7654
76.77874.96724.92435.19812.99733.89210.90282.8245-3.0585-2.836-0.2765-1.9270.7730.0019-0.63511.10.26060.02911.174-0.16391.1527-10.1622-44.780125.5195
84.3316-4.6244-4.52415.18415.29716.0693-0.37571.3256-0.0821-0.2006-0.69491.38650.4092-0.4351.03110.7141-0.0789-0.23140.71490.08490.8739-21.6271-34.683828.798
90.9658-2.99432.24219.9783-7.03445.2898-0.5065-1.82-0.57730.42650.49451.7120.3958-0.8531-0.12540.67280.11030.18050.95560.09650.4339-20.9891-31.439243.654
108.2456-0.67723.54133.29694.43538.43320.1020.6084-1.98171.8771-0.64630.54821.908-2.19470.85110.9323-0.12750.4541.16840.31640.8042-17.7215-45.367542.6961
116.21965.6149-5.26385.1113-5.50889.0123-0.09270.50181.22040.1985-0.05841.4553-0.5463-0.61770.05970.53670.1463-0.06460.5211-0.17670.7076-13.3503-1.805325.1461
124.2135-5.95380.97548.556-0.97991.8067-0.0922-1.56332.15740.6449-0.3075-1.6483-0.80420.4289-0.04820.6168-0.2033-0.19470.7241-0.03830.73975.91375.88522.5439
135.36941.43590.9227.53950.43445.140.1217-0.73320.0821.2082-0.2985-0.1874-0.06590.28980.13260.5153-0.054-0.06380.4177-0.00240.3044-5.2288-8.603331.1349
145.08672.9216-3.61065.0442-4.3485.2873-0.1685-0.36790.01650.0648-0.2161-0.5248-0.02940.79770.33180.4511-0.0059-0.09860.4217-0.05210.41710.8844-4.070923.0927
158.0953.2668-2.51078.8399-7.77148.57210.2932-0.06150.10220.33860.03420.7293-0.3602-0.4985-0.30970.42520.03920.04190.4167-0.09980.4131-16.5386-18.115230.0565
161.9481-1.68421.18493.3494-4.2137.6102-0.14430.16420.26810.2899-0.1811-0.4315-0.46510.50840.24810.4475-0.0504-0.06850.321-0.07270.4031-4.47328.391810.1046
174.07040.37255.58867.90642.08137.934-0.57113.02470.0139-1.78071.08382.9423-0.51360.5665-0.23221.0905-0.0787-0.16410.91790.07311.2692-24.27258.6958-16.4723
181.4396-0.9290.93534.079-2.0172.99210.0244-0.084-0.20070.3732-0.1350.35160.0268-0.15370.15460.3813-0.00080.05870.3217-0.06990.3829-14.84535.14752.7175
195.04951.81294.98964.53941.00765.43140.19220.59240.19890.1129-0.12890.21520.20170.42140.13960.3515-0.00240.04860.3248-0.02830.363-11.0585.2958-0.637
209.4743-1.59725.48175.3712-1.34257.4344-0.0697-0.03420.54150.0094-0.20810.1828-0.2158-0.40040.34130.39290.02920.04920.3468-0.06140.4036-18.329313.3492.4084
214.476-2.54933.86736.6681-6.11616.27120.74390.58350.1157-0.6198-0.2156-3.16580.88262.7183-0.01710.50370.0931-0.10960.6497-0.0290.98094.1683-25.8225.2832
222.32171.10111.7613.5221-1.88726.9775-0.03840.3309-0.2489-0.4929-0.0273-0.23440.91720.35990.05660.45320.08050.05490.3569-0.06850.3516-9.3562-26.70527.5359
231.82541.4109-1.61294.76260.21563.072-0.0204-0.32880.12140.17510.23610.15210.0452-0.0174-0.22170.31260.0186-0.07230.3556-0.02720.3121-12.4668-22.399720.0965
248.584-2.62655.63916.7596-4.96615.47090.38890.1649-0.1716-0.2048-0.2452-0.02620.49680.2334-0.1970.34110.0092-0.01760.36-0.00680.372-15.6882-28.964715.3276
254.6188-0.13472.27314.7907-0.67723.0549-0.5196-0.34420.1292-0.29640.31790.4472-0.3288-0.49680.19430.3568-0.00050.00340.341-0.01950.2659-14.3949-20.604610.2333
265.13542.32610.95234.51973.06297.04110.3637-0.3495-0.01130.47720.0453-0.2654-0.74581.0009-0.37470.26020.0183-0.04690.3626-0.00380.3793-3.9203-21.596522.4086
272.06550.1644-0.07882.1659-3.14596.08120.09240.1695-0.06030.26520.00770.46860.01530.0233-0.11710.29930.02570.01350.2741-0.02040.3277-14.6416-11.5406-8.0415
281.12540.56320.7062.7724-0.62175.4013-0.19540.31760.4071-0.41910.2751-0.019-0.72790.4952-0.00340.29560.007-0.02740.2731-0.02370.4131-7.829912.9825-7.758
297.05242.1852-4.21215.9041-3.3636.787-0.23910.39310.0375-0.39870.1922-0.2330.0902-0.05560.06090.2541-0.002-0.04360.2995-0.04320.3051-4.6973-3.56-12.9571
302.25662.14550.37317.0667-0.39450.2645-0.0710.15690.1549-0.24770.1053-0.1231-0.20710.01390.02780.28370.0030.01420.3055-0.02910.3407-6.59561.4522-11.7673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resid 26:35)
2X-RAY DIFFRACTION2(chain C and resid 36:53)
3X-RAY DIFFRACTION3(chain C and resid 54:76)
4X-RAY DIFFRACTION4(chain C and resid 77:85)
5X-RAY DIFFRACTION5(chain C and resid 86:100)
6X-RAY DIFFRACTION6(chain C and resid 101:111)
7X-RAY DIFFRACTION7(chain C and resid 112:117)
8X-RAY DIFFRACTION8(chain C and resid 118:124)
9X-RAY DIFFRACTION9(chain C and resid 125:135)
10X-RAY DIFFRACTION10(chain C and resid 136:146)
11X-RAY DIFFRACTION11(chain H and resid 4:13)
12X-RAY DIFFRACTION12(chain H and resid 14:20)
13X-RAY DIFFRACTION13(chain H and resid 21:83)
14X-RAY DIFFRACTION14(chain H and resid 84:100)
15X-RAY DIFFRACTION15(chain H and resid 101:117)
16X-RAY DIFFRACTION16(chain H and resid 118:138)
17X-RAY DIFFRACTION17(chain H and resid 139:147)
18X-RAY DIFFRACTION18(chain H and resid 148:180)
19X-RAY DIFFRACTION19(chain H and resid 181:200)
20X-RAY DIFFRACTION20(chain H and resid 201:226)
21X-RAY DIFFRACTION21(chain L and resid 1:6)
22X-RAY DIFFRACTION22(chain L and resid 7:28)
23X-RAY DIFFRACTION23(chain L and resid 29:58)
24X-RAY DIFFRACTION24(chain L and resid 59:79)
25X-RAY DIFFRACTION25(chain L and resid 80:93)
26X-RAY DIFFRACTION26(chain L and resid 94:106)
27X-RAY DIFFRACTION27(chain L and resid 107:120)
28X-RAY DIFFRACTION28(chain L and resid 121:139)
29X-RAY DIFFRACTION29(chain L and resid 140:158)
30X-RAY DIFFRACTION30(chain L and resid 159:216)

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