2ERJ | pdb_00002erj

Crystal structure of the heterotrimeric interleukin-2 receptor in complex with interleukin-2

PDB DOI:&nbsphttps://doi.org/10.2210/pdb2ERJ/pdb

Classification:&nbspIMMUNE SYSTEM/CYTOKINE
Organism(s):&nbspHomo sapiens
Expression System:&nbspTrichoplusia ni
Mutation(s):&nbspYes&nbsp

Deposited:&nbsp2005-10-25&nbspReleased:&nbsp2006-02-21&nbsp
Deposition Author(s):&nbspDebler, E.W., Stauber, D.J., Wilson, I.A.

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp3.00 Å
R-Value Free:&nbsp
0.263 (Depositor), 0.220 (DCC)&nbsp
R-Value Work:&nbsp
0.220 (Depositor), 0.220 (DCC)&nbsp
R-Value Observed:&nbsp
0.223&nbsp(Depositor)&nbsp

Starting Model: experimental
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wwPDB Validation&nbsp 3D Report&nbspFull Report

Ligand Structure Quality Assessment&nbsp

This is version 2.3 of the entry. See complete&nbsphistory.&nbsp

Literature

Crystal structure of the IL-2 signaling complex: Paradigm for a heterotrimeric cytokine receptor.

Stauber, D.J.,&nbspDebler, E.W.,&nbspHorton, P.A.,&nbspSmith, K.A.,&nbspWilson, I.A.

(2006) Proc Natl Acad Sci U S A&nbsp103: 2793

PubMed:&nbsp16477002&nbspSearch on PubMedSearch on PubMed Central
DOI:&nbsphttps://doi.org/10.1073/pnas.0511161103
Primary Citation of Related Structures: &nbsp
2ERJ

PubMed Abstract:&nbsp
IL-2 is a cytokine that functions as a growth factor and central regulator in the immune system and mediates its effects through ligand-induced hetero-trimerization of the receptor subunits IL-2R alpha, IL-2R beta, and gamma(c). Here, we describe the crystal structure of the trimeric assembly of the human IL-2 receptor ectodomains in complex with IL-2 at 3.0 A resolution. The quaternary structure is consistent with a stepwise assembly from IL-2/IL-2R alpha to IL-2/IL-2R alpha/IL-2R beta to IL-2/IL-2R alpha/IL-2R beta/gamma(c). The IL-2R alpha subunit forms the largest of the three IL-2/IL-2R interfaces, which, together with the high abundance of charge-charge interactions, correlates well with the rapid association rate and high-affinity interaction of IL-2R alpha with IL-2 at the cell surface. Surprisingly, IL-2R alpha makes no contacts with IL-2R beta or gamma(c), and only minor changes are observed in the IL-2 structure in response to receptor binding. These findings support the principal role of IL-2R alpha to deliver IL-2 to the signaling complex and act as regulator of signal transduction. Cooperativity in assembly of the final quaternary complex is easily explained by the extraordinarily extensive set of interfaces found within the fully assembled IL-2 signaling complex, which nearly span the entire length of the IL-2R beta and gamma(c) subunits. Helix A of IL-2 wedges tightly between IL-2R beta and gamma(c) to form a three-way junction that coalesces into a composite binding site for the final gamma(c) recruitment. The IL-2/gamma(c) interface itself exhibits the smallest buried surface and the fewest hydrogen bonds in the complex, which is consistent with its promiscuous use in other cytokine receptor complexes.

Organizational Affiliation

Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content&nbsp

Total Structure Weight: 196.17 kDa&nbsp
Atom Count: 11,187&nbsp
Modeled Residue Count: 1,318&nbsp
Deposited Residue Count: 1,648&nbsp
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor alpha chain	A, E	225	Homo sapiens	Mutation(s): 2&nbsp Gene Names:&nbspIL2RA
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01589&nbsp(Homo sapiens) Explore&nbspP01589&nbsp Go to UniProtKB: &nbspP01589
PHAROS: &nbspP01589 GTEx: &nbspENSG00000134460&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01589
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor beta chain	B, F	219	Homo sapiens	Mutation(s): 0&nbsp Gene Names:&nbspIL2RB
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP14784&nbsp(Homo sapiens) Explore&nbspP14784&nbsp Go to UniProtKB: &nbspP14784
PHAROS: &nbspP14784 GTEx: &nbspENSG00000100385&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14784
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain F	Go to GlyGen: P14784-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common gamma chain	C, G	247	Homo sapiens	Mutation(s): 1&nbsp Gene Names:&nbspIL2RG
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP31785&nbsp(Homo sapiens) Explore&nbspP31785&nbsp Go to UniProtKB: &nbspP31785
PHAROS: &nbspP31785 GTEx: &nbspENSG00000147168&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31785
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C Focus chain G	Go to GlyGen: P31785-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2	D, H	133	Homo sapiens	Mutation(s): 1&nbsp Gene Names:&nbspIL2
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP60568&nbsp(Homo sapiens) Explore&nbspP60568&nbsp Go to UniProtKB: &nbspP60568
PHAROS: &nbspP60568 GTEx: &nbspENSG00000109471&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60568
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, M	4		N-Glycosylation	Interactions Focus chain I Focus chain M Interactions & Density Focus chain I Focus chain M
Glycosylation Resources
GlyTouCan: &nbspG32152BH GlyCosmos: &nbspG32152BH GlyGen: &nbspG32152BH

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	J	2		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: &nbspG86851RC GlyCosmos: &nbspG86851RC GlyGen: &nbspG86851RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, O	3		N-Glycosylation	Interactions Focus chain K Focus chain O Interactions & Density Focus chain K Focus chain O
Glycosylation Resources
GlyTouCan: &nbspG15407YE GlyCosmos: &nbspG15407YE GlyGen: &nbspG15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, P	2		N-Glycosylation	Interactions Focus chain L Focus chain P Interactions & Density Focus chain L Focus chain P
Glycosylation Resources
GlyTouCan: &nbspG42666HT GlyCosmos: &nbspG42666HT GlyGen: &nbspG42666HT

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	N	3		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: &nbspG21290RB GlyCosmos: &nbspG21290RB GlyGen: &nbspG21290RB

Small Molecules

Ligands&nbsp1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File&nbsp SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth G] SDF format, chain T [auth G] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G]	Q [auth C], R [auth C], S [auth G], T [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth G] Focus chain T [auth G] Interactions & Density Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth G] Focus chain T [auth G]

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp3.00 Å
R-Value Free:&nbsp 0.263 (Depositor), 0.220 (DCC)&nbsp
R-Value Work:&nbsp 0.220 (Depositor), 0.220 (DCC)&nbsp
R-Value Observed:&nbsp0.223&nbsp(Depositor)&nbsp

Space Group:&nbspP 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.266	α = 83.85
b = 70.545	β = 82.45
c = 129.236	γ = 89.72

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View&nbspFull Validation Report

Ligand Structure Quality Assessment&nbsp

Entry History&nbsp

Deposition Data

Released Date:&nbsp2006-02-21&nbsp

Deposition Author(s):&nbsp

Debler, E.W.

Stauber, D.J.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2006-02-21
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2023-08-23
Changes: Data collection, Refinement description
Version 2.3: 2024-10-30
Changes: Structure summary