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- PDB-9e2t: Structure of a de novo designed interleukin-21 mimetic complex wi... -

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Basic information

Entry
Database: PDB / ID: 9e2t
TitleStructure of a de novo designed interleukin-21 mimetic complex with IL-21R and IL-2Rg
Components
  • 21h10
  • Cytokine receptor common subunit gamma
  • Interleukin-21 receptor
KeywordsDE NOVO PROTEIN/IMMUNE SYSTEM / cytokine / immunology / interleukin / DE NOVO PROTEIN / DE NOVO PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


interleukin-21 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of T cell differentiation in thymus / lymphocyte differentiation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway ...interleukin-21 receptor activity / mature B cell differentiation / interleukin-15 receptor activity / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of T cell differentiation in thymus / lymphocyte differentiation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / interleukin-15-mediated signaling pathway / cellular homeostasis / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / cytokine receptor activity / Interleukin-2 signaling / natural killer cell activation / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / cytokine binding / Interleukin receptor SHC signaling / coreceptor activity / Interleukin-7 signaling / positive regulation of phagocytosis / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / T cell differentiation in thymus / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / gene expression / receptor complex / endosome / immune response / external side of plasma membrane / cell surface / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
: / : / Cytokine receptor-like factor 2-like, D2 domain / Cytokine receptor-like factor 2, domain 1 / Short hematopoietin receptor family 1 signature. / Short hematopoietin receptor, family 1, conserved site / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Cytokine receptor common subunit gamma / Interleukin-21 receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsAbhiraman, G.C. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Sci Immunol / Year: 2025
Title: Design of a potent interleukin-21 mimic for cancer immunotherapy.
Authors: Chun, J.H. / Lim, B.S. / Roy, S. / Walsh, M.J. / Abhiraman, G.C. / Zhangxu, K. / Atajanova, T. / Revach, O.Y. / Clark, E.C. / Li, P. / Palin, C.A. / Khanna, A. / Tower, S. / Kureshi, R. / ...Authors: Chun, J.H. / Lim, B.S. / Roy, S. / Walsh, M.J. / Abhiraman, G.C. / Zhangxu, K. / Atajanova, T. / Revach, O.Y. / Clark, E.C. / Li, P. / Palin, C.A. / Khanna, A. / Tower, S. / Kureshi, R. / Hoffman, M.T. / Sharova, T. / Lawless, A. / Cohen, S. / Boland, G.M. / Nguyen, T. / Peprah, F. / Tello, J.G. / Liu, S.Y. / Kim, C.J. / Shin, H. / Quijano-Rubio, A. / Jude, K.M. / Gerben, S. / Murray, A. / Heine, P. / DeWitt, M. / Ulge, U.Y. / Carter, L. / King, N.P. / Silva, D.A. / Kueh, H.Y. / Kalia, V. / Sarkar, S. / Jenkins, R.W. / Garcia, K.C. / Leonard, W.J. / Dougan, M. / Dougan, S.K. / Baker, D.
History
DepositionOct 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 21h10
B: Interleukin-21 receptor
C: Cytokine receptor common subunit gamma
D: 21h10
E: Interleukin-21 receptor
F: Cytokine receptor common subunit gamma
G: 21h10
H: Interleukin-21 receptor
I: 21h10
J: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,50528
Polymers194,95510
Non-polymers2,54918
Water55831
1
A: 21h10
B: Interleukin-21 receptor
C: Cytokine receptor common subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,08212
Polymers60,8863
Non-polymers1,1959
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 21h10
E: Interleukin-21 receptor
F: Cytokine receptor common subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6127
Polymers60,8863
Non-polymers7264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 21h10
H: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8754
Polymers36,5912
Non-polymers2832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: 21h10
J: Interleukin-21 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9375
Polymers36,5912
Non-polymers3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.499, 78.082, 101.219
Angle α, β, γ (deg.)94.630, 103.390, 114.550
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 24 or resid 30...
d_2ens_1(chain "D" and (resid 3 through 41 or resid 43 through 49 or resid 57 through 99))
d_3ens_1(chain "G" and (resid 3 through 24 or resid 30...
d_4ens_1(chain "I" and (resid 3 through 24 or resid 30...
d_1ens_2(chain "B" and (resid 0 through 32 or resid 34 through 210))
d_2ens_2(chain "E" and (resid 0 through 32 or resid 34 or resid 43 through 208 or resid 210))
d_3ens_2(chain "H" and (resid 0 through 32 or resid 34 or resid 43 through 208 or resid 210))
d_4ens_2(chain "J" and (resid 0 through 32 or resid 34 or resid 43 through 208 or resid 210))
d_1ens_3(chain "C" and (resid 53 through 248 or resid 249 through 250))
d_2ens_3(chain "F" and (resid 53 through 97 or (resid 98...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUASPASPAA3 - 243 - 24
d_12ens_1THRTHRVALVALAA30 - 4130 - 41
d_13ens_1METMETARGARGAA43 - 4943 - 49
d_14ens_1SERSERGLYGLYAA57 - 9957 - 99
d_21ens_1GLUGLUVALVALDD3 - 413 - 41
d_22ens_1METMETARGARGDD43 - 4943 - 49
d_23ens_1SERSERGLYGLYDD57 - 9957 - 99
d_31ens_1GLUGLUASPASPGG3 - 243 - 24
d_32ens_1THRTHRVALVALGG30 - 4130 - 41
d_33ens_1METMETARGARGGG43 - 4943 - 49
d_34ens_1SERSERGLYGLYGG57 - 9957 - 99
d_41ens_1GLUGLUASPASPII3 - 243 - 24
d_42ens_1THRTHRVALVALII30 - 4130 - 41
d_43ens_1METMETARGARGII43 - 4943 - 49
d_44ens_1SERSERGLYGLYII57 - 9957 - 99
d_11ens_2PROPROTRPTRPBB0 - 323 - 35
d_12ens_2ASPASPSERSERBB34 - 20837 - 211
d_13ens_2NAGNAGNAGNAGBK301
d_21ens_2PROPROTRPTRPEE0 - 323 - 35
d_22ens_2ASPASPASPASPEE3437
d_23ens_2ALAALASERSEREE43 - 20846 - 211
d_24ens_2NAGNAGNAGNAGET301
d_31ens_2PROPROTRPTRPHH0 - 323 - 35
d_32ens_2ASPASPASPASPHH3437
d_33ens_2ALAALASERSERHH43 - 20846 - 211
d_34ens_2NAGNAGNAGNAGHX301
d_41ens_2PROPROTRPTRPJJ0 - 323 - 35
d_42ens_2ASPASPASPASPJJ3437
d_43ens_2ALAALASERSERJJ43 - 20846 - 211
d_44ens_2NAGNAGNAGNAGJZ301
d_11ens_3ASPASPSERSERCC53 - 2482 - 197
d_12ens_3NAGNAGNAGNAGCN301
d_13ens_3NAGNAGNAGNAGCO302
d_21ens_3ASPASPSERSERFF53 - 2482 - 197
d_22ens_3NAGNAGNAGNAGFV301
d_23ens_3NAGNAGNAGNAGFW302

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

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Protein , 3 types, 10 molecules ADGIBEHJCF

#1: Protein
21h10


Mass: 12186.134 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein
Interleukin-21 receptor / IL-21 receptor / IL-21R / Novel interleukin receptor


Mass: 24405.131 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL21R, NILR, UNQ3121/PRO10273 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HBE5
#3: Protein Cytokine receptor common subunit gamma / Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / ...Interleukin-2 receptor subunit gamma / IL-2 receptor subunit gamma / IL-2R subunit gamma / IL-2RG / gammaC / p64


Mass: 24295.094 Da / Num. of mol.: 2 / Fragment: residues 55-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P31785

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Sugars , 1 types, 9 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 40 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Potassium thiocyanate, 0.1M Bis-Tris propane, pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.28→48.238 Å / Num. obs: 84630 / % possible obs: 92.4 % / Redundancy: 5.6642 % / Biso Wilson estimate: 50.55 Å2 / CC1/2: 0.996 / Net I/σ(I): 5.17
Reflection shellResolution: 2.28→2.544 Å / Num. unique obs: 2417 / CC1/2: 0.342

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→41.17 Å / SU ML: 0.3162 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 1930 4 %random
Rwork0.1988 46351 --
obs0.2006 48281 52.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.09 Å2
Refinement stepCycle: LAST / Resolution: 2.28→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13048 0 162 31 13241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002813541
X-RAY DIFFRACTIONf_angle_d0.560718315
X-RAY DIFFRACTIONf_chiral_restr0.04021972
X-RAY DIFFRACTIONf_plane_restr0.0042339
X-RAY DIFFRACTIONf_dihedral_angle_d13.3775060
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.40927597104
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.1020206264
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.14949787498
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.807120126622
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.916766075054
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.798216093471
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS4.08541610406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.405950.2867116X-RAY DIFFRACTION1.85
2.34-2.40.2073110.3438269X-RAY DIFFRACTION4.34
2.4-2.470.4874300.3514717X-RAY DIFFRACTION11.44
2.47-2.550.3807560.33391342X-RAY DIFFRACTION21.46
2.55-2.640.3841850.34242019X-RAY DIFFRACTION32.12
2.64-2.750.37581000.31742442X-RAY DIFFRACTION39.01
2.75-2.870.37751270.30593037X-RAY DIFFRACTION48.35
2.87-3.020.33281520.30513676X-RAY DIFFRACTION58.47
3.02-3.210.32041830.27234403X-RAY DIFFRACTION70.39
3.21-3.460.28372160.21935184X-RAY DIFFRACTION82.54
3.46-3.810.27222240.19495366X-RAY DIFFRACTION85.71
3.81-4.360.20162520.16296069X-RAY DIFFRACTION96.59
4.36-5.490.18822490.15675968X-RAY DIFFRACTION95.32
5.49-41.170.20742400.17915743X-RAY DIFFRACTION91.44
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)
14.113029669080.454986032588-1.266523624645.4990623067-0.1354667861494.739630029570.108305904338-0.964498206798-0.7356875307410.758486666511-0.286882798064-0.9972446344451.017767586530.6619679607350.05964059545380.670467709932-0.038958770042-0.1119414458540.6548374648770.1203972170210.438073330713-42.509-34.05150.833
22.143624860650.6131150462710.089451594832.414028051620.7433369261145.020069369850.0502139057933-0.04453221326950.1517722628590.1941438658460.134155134463-0.1952409879850.080754316948-0.0599461929852-0.1701078770530.07840927841960.0670092281160.03209315932830.205576897863-0.03751284820240.267308166563-33.679-19.36828.281
32.290701432241.0262318449-2.056576739891.4872458975-1.430886931125.62487235765-0.1910571370560.172618742357-0.0569772163360.003577569969430.08949048006740.215911972140.07983184198230.06950308805210.09391076557670.1577200614760.05642525251880.02142710303330.16767903268-0.07291246633480.237715812814-66.219-39.40635.425
44.901130858851.32211921548-0.2550071981637.660589777060.1875948185694.16107638928-0.2319185353010.660460508844-0.333639462599-0.764347542923-0.03596677231240.1316809343470.2748787406480.4149378921140.2347054395150.369414053359-0.0126751633696-0.05314108867160.430085564918-0.005740982240440.224226504772-104.319-68.38465.364
52.878175533140.5603086209840.9360566185521.92748410984-0.2152306959664.567440904660.0549983241036-0.01286680191410.0114215732493-0.1704275427790.0169149554650.297193765146-0.0794549416003-0.0266386372485-0.0849400021940.214943272265-0.006006315844680.000813588873650.01453242995980.01176241741820.248894321777-119.877-74.28587.819
62.008243434931.28636054017-1.715983221271.89727773214-1.803429320924.256469997370.152310325003-0.2842279596280.172116715599-0.00146907264049-0.138446184776-0.0651796475850.1496535226820.162358993382-0.01337296773450.207861436092-0.0134080961241-0.01316070107850.1435377721-0.06292504572150.179939829663-87.243-53.24283.474
76.111605131460.4050886978591.054863718161.27703827261-0.5897568614560.642178283145-0.190518017092-0.03092156024010.1691308971830.5720999663270.0954725164677-0.57888811794-0.5979086810631.046969117430.1406807752440.734551054001-0.245116205185-0.1845479136541.01716675746-0.0180262441440.5981979979255.862-0.10939.75
82.576647867760.04032718201190.7648152303151.63450834455-1.054106340434.76471412645-0.0478109462586-0.120228219107-0.2518355547560.2633093350710.104179959832-0.0836843253305-0.0001059590453160.381703297793-0.0155712373930.1719357168190.06791208833390.02382775500380.21503655789-0.09149424971660.267763046416-13.101-13.26624.565
95.489235971122.89145198932-0.4042118253796.610610448910.5259833749082.88430385153-0.005825107972480.1224160672040.128821615561-0.628086674619-0.3702398097660.679562029933-0.189855749359-1.116299181220.3584517059320.57243763754-0.0341987474347-0.1811294143740.949780049283-0.1765890610710.534108705608-15.031-7.302-18.798
102.68692972588-0.128311656494-0.6721280662092.782037297641.074638129064.473679902270.1485940484780.0270307288997-0.0764294561817-0.284049427105-0.0985041292959-0.1413456371990.00885006642088-0.252395147195-0.03667826740890.218926384997-0.0693991198613-0.008862132640270.02214669552710.0524011387780.2277886419877.0490.689-4.558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:99 )A1 - 99
2X-RAY DIFFRACTION2( CHAIN B AND ( RESID 0:208 OR RESID 301:301 ) )B0 - 208
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 0:208 OR RESID 301:301 ) )B301
4X-RAY DIFFRACTION3( CHAIN C AND RESID 53:248 )C53 - 248
5X-RAY DIFFRACTION4( CHAIN D AND RESID 1:99 )D1 - 99
6X-RAY DIFFRACTION5( CHAIN E AND RESID 0:209 )E0 - 209
7X-RAY DIFFRACTION6( CHAIN F AND RESID 52:248 )F52 - 248
8X-RAY DIFFRACTION7( CHAIN G AND RESID 1:99 )G1 - 99
9X-RAY DIFFRACTION8( CHAIN H AND RESID 0:209 )H0 - 209
10X-RAY DIFFRACTION9( CHAIN I AND RESID 3:99 )I3 - 99
11X-RAY DIFFRACTION10( CHAIN J AND RESID -2:209 )J-2 - 209

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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