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- PDB-4zf7: Crystal structure of ferret interleukin-2 -

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Basic information

Entry
Database: PDB / ID: 4zf7
TitleCrystal structure of ferret interleukin-2
ComponentsInterleukin 2
KeywordsIMMUNE SYSTEM / ferret / interleukin-2
Function / homology
Function and homology information


positive regulation of immunoglobulin production => GO:0002639 / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / negative regulation of B cell apoptotic process / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production ...positive regulation of immunoglobulin production => GO:0002639 / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / negative regulation of B cell apoptotic process / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / adaptive immune response / 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; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Interleukin-2
Similarity search - Component
Biological speciesMustela putorius furo (domestic ferret)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.893 Å
AuthorsRen, B. / Newman, J. / McKinstry, W.J. / Adams, T.E.
CitationJournal: Dev.Comp.Immunol. / Year: 2015
Title: Structural and functional characterisation of ferret interleukin-2.
Authors: Ren, B. / McKinstry, W.J. / Pham, T. / Newman, J. / Layton, D.S. / Bean, A.G. / Chen, Z. / Laurie, K.L. / Borg, K. / Barr, I.G. / Adams, T.E.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin 2
B: Interleukin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0808
Polymers32,1552
Non-polymers9256
Water4,540252
1
A: Interleukin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6685
Polymers16,0771
Non-polymers5914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4123
Polymers16,0771
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.938, 92.938, 89.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

21B-416-

HOH

DetailsMonomer confirmed by chromatography

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Interleukin 2 / Uncharacterized protein


Mass: 16077.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mustela putorius furo (domestic ferret)
Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A3FBE6

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Non-polymers , 5 types, 258 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 M ammonium sulfate and 0.1 M sodium citrate - citric acid buffer at pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→32.206 Å / Num. obs: 35935 / % possible obs: 99.9 % / Redundancy: 10.8 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Blu-Icedata collection
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.893→32.206 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 1910 5.61 %
Rwork0.165 --
obs0.1668 34017 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.893→32.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 56 252 2359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022148
X-RAY DIFFRACTIONf_angle_d1.6492883
X-RAY DIFFRACTIONf_dihedral_angle_d15.031824
X-RAY DIFFRACTIONf_chiral_restr0.1344
X-RAY DIFFRACTIONf_plane_restr0.008348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8931-1.94050.30641290.2562103X-RAY DIFFRACTION89
1.9405-1.99290.2561230.21362031X-RAY DIFFRACTION86
1.9929-2.05160.221330.18592257X-RAY DIFFRACTION93
2.0516-2.11780.22771360.17062285X-RAY DIFFRACTION95
2.1178-2.19350.21581270.16352238X-RAY DIFFRACTION94
2.1935-2.28130.2131340.17892216X-RAY DIFFRACTION93
2.2813-2.3850.2051330.16642250X-RAY DIFFRACTION93
2.385-2.51070.19681340.15612293X-RAY DIFFRACTION95
2.5107-2.6680.18771410.15832310X-RAY DIFFRACTION96
2.668-2.87390.19921340.16482339X-RAY DIFFRACTION97
2.8739-3.16280.21461450.16652376X-RAY DIFFRACTION98
3.1628-3.620.17751410.15462399X-RAY DIFFRACTION99
3.62-4.55870.15761490.13862450X-RAY DIFFRACTION99
4.5587-32.21060.19711510.17132560X-RAY DIFFRACTION99
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)
14.43712.1224-1.68695.6768-1.55664.6687-0.018-0.13090.21220.1155-0.0215-0.0042-0.06880.00470.01560.1956-0.0769-0.06130.1444-0.0620.184830.578-26.5518-2.6265
25.6182-0.3077-1.48793.16530.04792.9485-0.0067-0.0498-0.17120.173-0.02890.03470.0539-0.05140.03670.1978-0.0687-0.02840.1155-0.00970.145927.5203-35.1742-4.9406
33.2117-0.28641.81720.2960.42392.2945-0.6658-0.43590.51730.0005-0.24410.3690.1429-0.3166-0.34440.51620.530.45690.59530.2541.257612.5906-23.7437-1.7399
47.9508-0.227-2.44765.44590.77886.2114-0.00940.18670.2072-0.2458-0.03210.5189-0.303-0.38960.00980.2364-0.0524-0.05480.1493-0.00250.187924.1252-27.481-11.8197
52.4071-0.948-1.30715.17811.21633.3529-0.105-0.4224-0.2220.4764-0.0322-0.23680.25480.5810.06770.1736-0.0742-0.07880.24830.00130.213835.5743-39.611-1.5853
63.40940.6985-0.52475.30060.21532.38650.1621-0.23640.12160.1463-0.0442-0.38060.00260.1874-0.07990.234-0.0735-0.06380.1503-0.03650.232937.5613-27.0878-1.1839
75.6758-0.09982.54853.77150.66853.8236-0.12550.32840.075-0.3036-0.0030.37570.007-0.08580.03060.2087-0.0619-0.01340.1403-0.0160.185235.3902-12.3215-3.6574
85.12420.8103-0.41683.00582.08825.42370.01160.12680.1578-0.4542-0.23570.6968-0.3862-0.47520.21810.2372-0.0113-0.07080.1428-0.00920.245936.09850.91464.8171
92.7552-3.78981.07846.3515-0.81741.9163-0.05010.1692-0.1052-0.51840.0790.0978-0.26030.0932-0.01410.3183-0.07340.00170.1688-0.02650.19543.6583-2.1301-4.336
106.875-0.68381.99426.5010.2382.99-0.22610.5557-0.0602-0.36810.1337-0.8402-0.0030.3065-0.04620.2941-0.10020.0390.2091-0.06620.272444.5358-12.7668-8.027
110.680.3572-0.73282.7947-0.48291.1940.19360.28230.22780.09340.48550.5619-0.754-0.5920.31620.958-0.0645-0.24230.65580.22240.470634.77046.6814-14.5047
123.1759-0.6352-0.72975.5234-2.16898.88120.05480.07740.0926-0.14910.31850.2636-0.5096-0.6164-0.29080.1519-0.0223-0.030.11630.00160.199736.88514.70034.782
136.7076-0.87633.34475.28230.05853.8173-0.069-0.19190.274-0.2233-0.25641.05680.0306-0.80810.21550.2142-0.0091-0.05060.2521-0.06740.35529.1391-5.81580.5908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 94 )
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 112 )
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 132 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 50 )
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 95 )
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 100 )
12X-RAY DIFFRACTION12chain 'B' and (resid 101 through 112 )
13X-RAY DIFFRACTION13chain 'B' and (resid 113 through 132 )

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