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

ID or keywords:

Entry

Database: PDB / ID: 9e2t

Title

Structure 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

Keywords

DE 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 ...
Similarity search - Function

Biological species

synthetic construct (others)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Abhiraman, G.C. / Jude, K.M. / Garcia, K.C.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: De novo mimetic protein of interleukin-21 shows outstanding therapeutic efficacy in cancer.
Authors: Chun, J.H. / Zhangxu, K. / Roy, S. / Abhiraman, G.C. / Garcia, K.C. / Dougan, S.K. / Leonard, W. / Dougan, M. / Baker, D.

History

Deposition	Oct 22, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9e2t.cif.gz	799.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9e2t.ent.gz	557.7 KB	Display	PDB format
PDBx/mmJSON format	9e2t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9e2t_validation.pdf.gz	542.2 KB	Display	wwPDB validaton report
Full document	9e2t_full_validation.pdf.gz	563.3 KB	Display
Data in XML	9e2t_validation.xml.gz	64.1 KB	Display
Data in CIF	9e2t_validation.cif.gz	81.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e2/9e2t ftp://data.pdbj.org/pub/pdb/validation_reports/e2/9e2t	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/1148 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1) #149 - May 2012 Leptin similarity (1) #122 - Feb 2010 Enhanceosome similarity (2) #148 - Apr 2012 Ras Protein similarity (2)

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

198 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 21h10

B: Interleukin-21 receptor

C: Cytokine receptor common subunit gamma

hetero molecules

defined by author
Evidence: assay for oligomerization, signaling assays to confirm ligand dependent receptor dimerization
62.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: 21h10

E: Interleukin-21 receptor

F: Cytokine receptor common subunit gamma

hetero molecules

defined by author
61.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: 21h10

H: Interleukin-21 receptor

hetero molecules

defined by author
36.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

I: 21h10

J: Interleukin-21 receptor

hetero molecules

defined by author
36.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1
Space group name Hall	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 3 through 24 or resid 30...
d_2	ens_1	(chain "D" and (resid 3 through 41 or resid 43 through 49 or resid 57 through 99))
d_3	ens_1	(chain "G" and (resid 3 through 24 or resid 30...
d_4	ens_1	(chain "I" and (resid 3 through 24 or resid 30...
d_1	ens_2	(chain "B" and (resid 0 through 32 or resid 34 through 210))
d_2	ens_2	(chain "E" and (resid 0 through 32 or resid 34 or resid 43 through 208 or resid 210))
d_3	ens_2	(chain "H" and (resid 0 through 32 or resid 34 or resid 43 through 208 or resid 210))
d_4	ens_2	(chain "J" and (resid 0 through 32 or resid 34 or resid 43 through 208 or resid 210))
d_1	ens_3	(chain "C" and (resid 53 through 248 or resid 249 through 250))
d_2	ens_3	(chain "F" and (resid 53 through 97 or (resid 98...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ens_1	GLU	GLU	ASP	ASP	A	A	3 - 24	3 - 24
d_1	2	ens_1	THR	THR	VAL	VAL	A	A	30 - 41	30 - 41
d_1	3	ens_1	MET	MET	ARG	ARG	A	A	43 - 49	43 - 49
d_1	4	ens_1	SER	SER	GLY	GLY	A	A	57 - 99	57 - 99
d_2	1	ens_1	GLU	GLU	VAL	VAL	D	D	3 - 41	3 - 41
d_2	2	ens_1	MET	MET	ARG	ARG	D	D	43 - 49	43 - 49
d_2	3	ens_1	SER	SER	GLY	GLY	D	D	57 - 99	57 - 99
d_3	1	ens_1	GLU	GLU	ASP	ASP	G	G	3 - 24	3 - 24
d_3	2	ens_1	THR	THR	VAL	VAL	G	G	30 - 41	30 - 41
d_3	3	ens_1	MET	MET	ARG	ARG	G	G	43 - 49	43 - 49
d_3	4	ens_1	SER	SER	GLY	GLY	G	G	57 - 99	57 - 99
d_4	1	ens_1	GLU	GLU	ASP	ASP	I	I	3 - 24	3 - 24
d_4	2	ens_1	THR	THR	VAL	VAL	I	I	30 - 41	30 - 41
d_4	3	ens_1	MET	MET	ARG	ARG	I	I	43 - 49	43 - 49
d_4	4	ens_1	SER	SER	GLY	GLY	I	I	57 - 99	57 - 99
d_1	1	ens_2	PRO	PRO	TRP	TRP	B	B	0 - 32	3 - 35
d_1	2	ens_2	ASP	ASP	SER	SER	B	B	34 - 208	37 - 211
d_1	3	ens_2	NAG	NAG	NAG	NAG	B	K	301
d_2	1	ens_2	PRO	PRO	TRP	TRP	E	E	0 - 32	3 - 35
d_2	2	ens_2	ASP	ASP	ASP	ASP	E	E	34	37
d_2	3	ens_2	ALA	ALA	SER	SER	E	E	43 - 208	46 - 211
d_2	4	ens_2	NAG	NAG	NAG	NAG	E	T	301
d_3	1	ens_2	PRO	PRO	TRP	TRP	H	H	0 - 32	3 - 35
d_3	2	ens_2	ASP	ASP	ASP	ASP	H	H	34	37
d_3	3	ens_2	ALA	ALA	SER	SER	H	H	43 - 208	46 - 211
d_3	4	ens_2	NAG	NAG	NAG	NAG	H	X	301
d_4	1	ens_2	PRO	PRO	TRP	TRP	J	J	0 - 32	3 - 35
d_4	2	ens_2	ASP	ASP	ASP	ASP	J	J	34	37
d_4	3	ens_2	ALA	ALA	SER	SER	J	J	43 - 208	46 - 211
d_4	4	ens_2	NAG	NAG	NAG	NAG	J	Z	301
d_1	1	ens_3	ASP	ASP	SER	SER	C	C	53 - 248	2 - 197
d_1	2	ens_3	NAG	NAG	NAG	NAG	C	N	301
d_1	3	ens_3	NAG	NAG	NAG	NAG	C	O	302
d_2	1	ens_3	ASP	ASP	SER	SER	F	F	53 - 248	2 - 197
d_2	2	ens_3	NAG	NAG	NAG	NAG	F	V	301
d_2	3	ens_3	NAG	NAG	NAG	NAG	F	W	302

NCS ensembles :

ID
ens_1
ens_2
ens_3

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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

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 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 interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.74 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.28→48.238 Å / Num. obs: 84630 / % possible obs: 92.4 % / Redundancy: 5.6642 % / B_iso Wilson estimate: 50.55 Å² / CC_1/2: 0.996 / Net I/σ(I): 5.17
Reflection shell	Resolution: 2.28→2.544 Å / Num. unique obs: 2417 / CC_1/2: 0.342

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2422	1930	4 %	random
R_work	0.1988	46351	-	-
obs	0.2006	48281	52.78 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 61.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→41.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13048	0	162	31	13241

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	13541
X-RAY DIFFRACTION	f_angle_d	0.5607	18315
X-RAY DIFFRACTION	f_chiral_restr	0.0402	1972
X-RAY DIFFRACTION	f_plane_restr	0.004	2339
X-RAY DIFFRACTION	f_dihedral_angle_d	13.377	5060

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	1.40927597104
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	1.1020206264
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	1.14949787498
ens_2	d_2	B	B	X-RAY DIFFRACTION	Torsion NCS	0.807120126622
ens_2	d_3	B	B	X-RAY DIFFRACTION	Torsion NCS	0.916766075054
ens_2	d_4	B	B	X-RAY DIFFRACTION	Torsion NCS	0.798216093471
ens_3	d_2	C	C	X-RAY DIFFRACTION	Torsion NCS	4.08541610406

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.28-2.34	0.4059	5	0.2867	116	X-RAY DIFFRACTION	1.85
2.34-2.4	0.2073	11	0.3438	269	X-RAY DIFFRACTION	4.34
2.4-2.47	0.4874	30	0.3514	717	X-RAY DIFFRACTION	11.44
2.47-2.55	0.3807	56	0.3339	1342	X-RAY DIFFRACTION	21.46
2.55-2.64	0.3841	85	0.3424	2019	X-RAY DIFFRACTION	32.12
2.64-2.75	0.3758	100	0.3174	2442	X-RAY DIFFRACTION	39.01
2.75-2.87	0.3775	127	0.3059	3037	X-RAY DIFFRACTION	48.35
2.87-3.02	0.3328	152	0.3051	3676	X-RAY DIFFRACTION	58.47
3.02-3.21	0.3204	183	0.2723	4403	X-RAY DIFFRACTION	70.39
3.21-3.46	0.2837	216	0.2193	5184	X-RAY DIFFRACTION	82.54
3.46-3.81	0.2722	224	0.1949	5366	X-RAY DIFFRACTION	85.71
3.81-4.36	0.2016	252	0.1629	6069	X-RAY DIFFRACTION	96.59
4.36-5.49	0.1882	249	0.1567	5968	X-RAY DIFFRACTION	95.32
5.49-41.17	0.2074	240	0.1791	5743	X-RAY DIFFRACTION	91.44

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	4.11302966908	0.454986032588	-1.26652362464	5.4990623067	-0.135466786149	4.73963002957	0.108305904338	-0.964498206798	-0.735687530741	0.758486666511	-0.286882798064	-0.997244634445	1.01776758653	0.661967960735	0.0596405954538	0.670467709932	-0.038958770042	-0.111941445854	0.654837464877	0.120397217021	0.438073330713	-42.509	-34.051	50.833
2	2.14362486065	0.613115046271	0.08945159483	2.41402805162	0.743336926114	5.02006936985	0.0502139057933	-0.0445322132695	0.151772262859	0.194143865846	0.134155134463	-0.195240987985	0.080754316948	-0.0599461929852	-0.170107877053	0.0784092784196	0.067009228116	0.0320931593283	0.205576897863	-0.0375128482024	0.267308166563	-33.679	-19.368	28.281
3	2.29070143224	1.0262318449	-2.05657673989	1.4872458975	-1.43088693112	5.62487235765	-0.191057137056	0.172618742357	-0.056977216336	0.00357756996943	0.0894904800674	0.21591197214	0.0798318419823	0.0695030880521	0.0939107655767	0.157720061476	0.0564252525188	0.0214271030333	0.16767903268	-0.0729124663348	0.237715812814	-66.219	-39.406	35.425
4	4.90113085885	1.32211921548	-0.255007198163	7.66058977706	0.187594818569	4.16107638928	-0.231918535301	0.660460508844	-0.333639462599	-0.764347542923	-0.0359667723124	0.131680934347	0.274878740648	0.414937892114	0.234705439515	0.369414053359	-0.0126751633696	-0.0531410886716	0.430085564918	-0.00574098224044	0.224226504772	-104.319	-68.384	65.364
5	2.87817553314	0.560308620984	0.936056618552	1.92748410984	-0.215230695966	4.56744090466	0.0549983241036	-0.0128668019141	0.0114215732493	-0.170427542779	0.016914955465	0.297193765146	-0.0794549416003	-0.0266386372485	-0.084940002194	0.214943272265	-0.00600631584468	0.00081358887365	0.0145324299598	0.0117624174182	0.248894321777	-119.877	-74.285	87.819
6	2.00824343493	1.28636054017	-1.71598322127	1.89727773214	-1.80342932092	4.25646999737	0.152310325003	-0.284227959628	0.172116715599	-0.00146907264049	-0.138446184776	-0.065179647585	0.149653522682	0.162358993382	-0.0133729677345	0.207861436092	-0.0134080961241	-0.0131607010785	0.1435377721	-0.0629250457215	0.179939829663	-87.243	-53.242	83.474
7	6.11160513146	0.405088697859	1.05486371816	1.27703827261	-0.589756861456	0.642178283145	-0.190518017092	-0.0309215602401	0.169130897183	0.572099966327	0.0954725164677	-0.57888811794	-0.597908681063	1.04696911743	0.140680775244	0.734551054001	-0.245116205185	-0.184547913654	1.01716675746	-0.018026244144	0.598197997925	5.862	-0.109	39.75
8	2.57664786776	0.0403271820119	0.764815230315	1.63450834455	-1.05410634043	4.76471412645	-0.0478109462586	-0.120228219107	-0.251835554756	0.263309335071	0.104179959832	-0.0836843253305	-0.000105959045316	0.381703297793	-0.015571237393	0.171935716819	0.0679120883339	0.0238277550038	0.21503655789	-0.0914942497166	0.267763046416	-13.101	-13.266	24.565
9	5.48923597112	2.89145198932	-0.404211825379	6.61061044891	0.525983374908	2.88430385153	-0.00582510797248	0.122416067204	0.128821615561	-0.628086674619	-0.370239809766	0.679562029933	-0.189855749359	-1.11629918122	0.358451705932	0.57243763754	-0.0341987474347	-0.181129414374	0.949780049283	-0.176589061071	0.534108705608	-15.031	-7.302	-18.798
10	2.68692972588	-0.128311656494	-0.672128066209	2.78203729764	1.07463812906	4.47367990227	0.148594048478	0.0270307288997	-0.0764294561817	-0.284049427105	-0.0985041292959	-0.141345637199	0.00885006642088	-0.252395147195	-0.0366782674089	0.218926384997	-0.0693991198613	-0.00886213264027	0.0221466955271	0.052401138778	0.227788641987	7.049	0.689	-4.558

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:99 )	A	1 - 99
2	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 0:208 OR RESID 301:301 ) )	B	0 - 208
3	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 0:208 OR RESID 301:301 ) )	B	301
4	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 53:248 )	C	53 - 248
5	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 1:99 )	D	1 - 99
6	X-RAY DIFFRACTION	5	( CHAIN E AND RESID 0:209 )	E	0 - 209
7	X-RAY DIFFRACTION	6	( CHAIN F AND RESID 52:248 )	F	52 - 248
8	X-RAY DIFFRACTION	7	( CHAIN G AND RESID 1:99 )	G	1 - 99
9	X-RAY DIFFRACTION	8	( CHAIN H AND RESID 0:209 )	H	0 - 209
10	X-RAY DIFFRACTION	9	( CHAIN I AND RESID 3:99 )	I	3 - 99
11	X-RAY DIFFRACTION	10	( CHAIN J AND RESID -2:209 )	J	-2 - 209

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Protein , 3 types, 10 molecules ADGIBEHJCF

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Sugars , 1 types, 9 molecules

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Non-polymers , 2 types, 40 molecules

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-Protein , 3 types, 10 molecules ADGIBEHJCF

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-Non-polymers , 2 types, 40 molecules

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Protein , 3 types, 10 molecules ADGIBEHJCF

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Sugars , 1 types, 9 molecules

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Non-polymers , 2 types, 40 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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