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- PDB-7raa: Designed StabIL-2 seq15 -

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Basic information

Entry
Database: PDB / ID: 7raa
TitleDesigned StabIL-2 seq15
ComponentsInterleukin-2
KeywordsCYTOKINE / computational design
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 / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...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 / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / positive regulation of regulatory T cell differentiation / : / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / 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 differentiation / Interleukin receptor SHC signaling / 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 inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsJude, K.M. / Chu, A.E. / Huang, P.-S. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI051321 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Interleukin-2 superkines by computational design.
Authors: Ren, J. / Chu, A.E. / Jude, K.M. / Picton, L.K. / Kare, A.J. / Su, L. / Montano Romero, A. / Huang, P.S. / Garcia, K.C.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 3, 2024Group: 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
A: Interleukin-2
B: Interleukin-2
C: Interleukin-2
D: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3936
Polymers62,3444
Non-polymers492
Water27015
1
A: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6102
Polymers15,5861
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6102
Polymers15,5861
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,5861
Polymers15,5861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Interleukin-2


Theoretical massNumber of molelcules
Total (without water)15,5861
Polymers15,5861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.372, 66.372, 298.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 16 or resid 18...
d_2ens_1(chain "B" and (resid 5 through 16 or resid 18...
d_3ens_1(chain "C" and (resid 5 through 16 or resid 18...
d_4ens_1(chain "D" and (resid 5 through 16 or resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRLEUA4 - 15
d_12ens_1METASNA17 - 23
d_13ens_1PROLYSA28 - 29
d_14ens_1THRTHRA31
d_15ens_1METMETA33
d_16ens_1THRPROA35 - 41
d_17ens_1LYSTHRA43 - 45
d_18ens_1LEULEUA47
d_19ens_1HISGLUA49 - 61
d_110ens_1ALAALAA63 - 67
d_111ens_1ASPGLYA70 - 87
d_112ens_1CYSASPA92 - 96
d_113ens_1THRLEUA98 - 119
d_21ens_1THRLEUB6 - 17
d_22ens_1METASNB19 - 25
d_23ens_1PROLYSB30 - 31
d_24ens_1THRTHRB33
d_25ens_1METMETB35
d_26ens_1THRPROB37 - 43
d_27ens_1LYSTHRB45 - 47
d_28ens_1LEULEUB49
d_29ens_1HISGLUB51 - 63
d_210ens_1ALAALAB65 - 69
d_211ens_1ASPGLYB77 - 94
d_212ens_1CYSASPB97 - 101
d_213ens_1THRLEUB103 - 124
d_31ens_1THRLEUC6 - 17
d_32ens_1METASNC19 - 25
d_33ens_1PROLYSC30 - 31
d_34ens_1THRTHRC33
d_35ens_1METMETC35
d_36ens_1THRPROC37 - 43
d_37ens_1LYSTHRC45 - 47
d_38ens_1LEULEUC49
d_39ens_1HISGLUC51 - 63
d_310ens_1ALAALAC65 - 69
d_311ens_1ASPGLYC77 - 94
d_312ens_1CYSASPC101 - 105
d_313ens_1THRLEUC107 - 128
d_41ens_1THRLEUD5 - 16
d_42ens_1METASND18 - 24
d_43ens_1PROLYSD29 - 30
d_44ens_1THRTHRD32
d_45ens_1METMETD34
d_46ens_1THRPROD36 - 42
d_47ens_1LYSTHRD44 - 46
d_48ens_1LEULEUD48
d_49ens_1HISGLUD50 - 62
d_410ens_1ALAALAD64 - 68
d_411ens_1ASPGLYD70 - 87
d_412ens_1CYSASPD94 - 98
d_413ens_1THRLEUD100 - 121

NCS oper:
IDCodeMatrixVector
1given(0.328580020841, 0.338326773103, 0.881799390171), (-0.619012037741, -0.628015697939, 0.471614652311), (0.713343722924, -0.700807589674, 0.00307493412318)-22.9463356503, 94.7858185987, 39.5913832467
2given(-0.274101270308, -0.315509107848, -0.908472617353), (0.541383561706, 0.73012727917, -0.41691485381), (0.794841073882, -0.606109032334, -0.0293173701497)75.8317121901, 20.3782193479, 34.010788557
3given(-0.993013782955, -0.111340944472, 0.0390745562334), (0.106124090439, -0.987471106366, -0.116783952327), (0.0515878308258, -0.111821322549, 0.992388375352)60.3307475116, 119.702826121, 6.92752179549

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Components

#1: Protein
Interleukin-2 / IL-2 / T-cell growth factor / TCGF


Mass: 15586.066 Da / Num. of mol.: 4 / Mutation: G27M, I28L, K32D, V69A, L72Q, R81D, V115I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60568
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.3, 24% PEG 3350 with microseeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→44.77 Å / Num. obs: 13754 / % possible obs: 70.56 % / Redundancy: 27.4 % / Biso Wilson estimate: 85.58 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.105 / Rsym value: 0.103 / Net I/σ(I): 16.3
Reflection shellResolution: 2.69→2.9 Å / Redundancy: 25.2 % / Mean I/σ(I) obs: 0.16 / Num. unique obs: 688 / CC1/2: 0.528 / CC star: 0.458 / Rpim(I) all: 0.623 / Rrim(I) all: 3.205 / Rsym value: 3.141 / % possible all: 18.07

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSJan 31, 2020data reduction
XDSJan 31, 2020data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in silico predicted model

Resolution: 2.69→44.77 Å / SU ML: 0.3008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 822 5.98 %random selection
Rwork0.2504 12927 --
obs0.2531 13749 70.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.8 Å2
Refinement stepCycle: LAST / Resolution: 2.69→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 2 15 4063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244104
X-RAY DIFFRACTIONf_angle_d0.50465542
X-RAY DIFFRACTIONf_chiral_restr0.0342668
X-RAY DIFFRACTIONf_plane_restr0.0038692
X-RAY DIFFRACTIONf_dihedral_angle_d14.16731573
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.903466417272
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.930094673526
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.7961204877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.860.4394290.3741494X-RAY DIFFRACTION16.56
2.86-3.080.3928600.3328998X-RAY DIFFRACTION33.58
3.08-3.390.41261330.32292055X-RAY DIFFRACTION68.74
3.39-3.890.31531940.26913032X-RAY DIFFRACTION99.78
3.89-4.890.26951960.22863067X-RAY DIFFRACTION100
4.89-44.770.27832100.24043281X-RAY DIFFRACTION99.91
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)
13.75994797038-2.25914605636-0.4600524245632.28381643054-0.6919348038854.881377001010.6129735401190.184869677046-0.0123913408319-0.3198814301730.0452198868117-0.5829012332210.8957526148451.18739036446-0.03474382497210.5795567706280.589786110894-0.04600573688180.751747648465-0.3439350577380.27095693981722.217431920435.15913389913.56703756633
29.78304173893-5.76002431494-4.479982570488.633163158971.841490719782.172488941591.82814023593-0.379637546137-0.636847234419-0.653081295850.622460228738-2.3153068089-2.184535961411.8482991383-2.506313070311.750100930.04973263782450.4240644660771.65051442397-0.2601414010652.1373384390937.911248472550.523091713910.0713179618
35.58621248121-1.792612465650.2385056491866.327176282080.5647299346614.68994217190.0142375165848-0.2747848566750.231243729942-0.6726186010740.04836022664520.729157899322-0.0750076109975-0.0129917621559-0.08384323009350.2399620061560.418604812233-0.1191439836260.469215175555-0.1619145633280.42289429743319.485612301442.283450636713.5519539093
46.50970013489-2.01772956932.421458176085.2318831981-0.3628469361266.124384005070.0659553002635-0.178981709145-1.20803240497-0.0690174663888-0.01016615516060.1199691265760.719672283830.0604389782665-0.02303509337980.3522250896860.604250563148-0.1115686445750.62609288789-0.0268527525360.62316771962122.073358127633.137079296316.2733634148
53.01828888873-2.03026618644-0.5987442654332.468939788741.593737139751.92007889160.649278532336-0.09954181311781.18844617449-0.674913728912-0.2613599430360.347547897808-0.8024730124260.210108832548-0.09801649124450.5551862834580.3011412150250.6601479934170.3128653948450.1434609711530.8790793486398.2940832603460.661596545228.0797760847
67.217193811354.95701510178-4.999925534844.47970119231-1.858622859948.35295183530.2306319750480.467727192158-1.37502746336-0.261838050164-0.2293420309951.19651218397-0.233119909715-0.7899044383810.1496829368641.829282538960.660334242477-0.3632185157820.838119581287-0.3803875765591.456026767677.4862372079947.072386981422.5326054666
73.449620237941.613812497172.177208559411.241761291160.5628139191476.003579886920.0686549725447-0.3509501832261.22530797418-0.00569590137764-0.3607757432810.628585564076-1.10630995785-0.638883677435-0.6381090009090.7091833826950.5316083169230.7806156900190.3538275515490.002798387361970.7030842808227.260839602466.932726953829.4402855289
82.04650099321-3.05695341516-1.324828922035.507840583060.7153472245377.99699508252-0.0837211795558-0.430829313752-0.130480860552-0.2524193391850.026679457970.0227859902370.21622406804-0.0295438712809-0.1215579321090.3387971663180.3887100151880.02536836692570.7357175745640.02305835313330.76845582709154.113154440257.990488639331.2269944846
96.43386703635-6.110336225740.7719405476396.83161896248-1.712169750242.402424287510.8074165572331.15410379323-0.0383863597627-1.26655522348-0.627474508093-0.4323235774240.308855983309-0.28645850868-0.1412603275680.6069991806090.314697052824-0.1760456143290.7297031964390.01967254036430.43014746566544.152048828559.425031115524.5453719653
103.87978045005-0.5519268038121.213055614171.86563455205-0.139710632824.670292960860.425854207802-0.0371688824661-0.917958299477-0.56744848324-0.1183355617280.4532572240550.8601309618760.208470267558-1.87119706870.5546027642080.671845892222-0.5389642345050.5940224303420.06922890245250.32692147964945.682091495548.311732245829.2139160653
113.2254476552-1.94914647324-0.3141444727126.738281809430.2547783064188.676525422170.1563965318460.03802652364790.205040694657-0.2651284713920.4746844899850.354466836488-1.15519103191-1.17385188121-0.6962491842430.5708576062740.2764479604910.1571046070250.4845574943770.2558325592350.32980565455134.684169208687.18071623627.67554630033
125.66503659291-4.55792915438-2.136770600936.32185907743.260371496011.700807851210.2742485120591.91237408781-0.231538022986-1.43658762669-0.7868565587742.39533115309-0.6028457289890.0227923551476-0.113894615651.331960432540.196491377837-0.00981062741081.877460860870.6042270709881.3926910015519.547013076772.795290691616.4684492651
135.65951398097-2.54085837924-0.9094231604535.979828016470.7949118440444.1627609160.0778449366004-0.6679968200110.484499510672-0.1175459099710.226445448388-0.740139139701-0.2238502466730.271197870135-0.2395735354770.3722332513520.6064498353610.1174072807720.6871157757220.1043840865580.48154504241737.822506034682.643474754418.000284267
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 2:24)AA2 - 241 - 23
22(chain A and resid 25:32)AA25 - 3224 - 31
33(chain A and resid 33:96)AA33 - 9632 - 88
44(chain A and resid 97:128)AA97 - 12889 - 120
55(chain B and resid 0:67)BB0 - 671 - 68
66(chain B and resid 68:79)BB68 - 7969 - 80
77(chain B and resid 80:128)BB80 - 12881 - 125
88(chain C and resid 0:27)CC0 - 271 - 28
99(chain C and resid 28:90)CC28 - 9029 - 91
1010(chain C and resid 91:128)CC91 - 12892 - 129
1111(chain D and resid 1:24)DD1 - 241 - 24
1212(chain D and resid 25:37)DD25 - 3725 - 37
1313(chain D and resid 38:128)DD38 - 12838 - 122

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