3LQM | pdb_00003lqm

Structure of the IL-10R2 Common Chain

PDB DOI: https://doi.org/10.2210/pdb3LQM/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2010-02-09 Released: 2010-05-26
Deposition Author(s): Yoon, S.I., Walter, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.239 (Depositor), 0.242 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure and mechanism of receptor sharing by the IL-10R2 common chain.

Yoon, S.I., Jones, B.C., Logsdon, N.J., Harris, B.D., Deshpande, A., Radaeva, S., Halloran, B.A., Gao, B., Walter, M.R.

(2010) Structure 18: 638-648

PubMed: 20462497 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2010.02.009
Primary Citation Related Structures:
3LQM

PubMed Abstract:
IL-10R2 is a shared cell surface receptor required for the activation of five class 2 cytokines (IL-10, IL-22, IL-26, IL-28, and IL-29) that play critical roles in host defense. To define the molecular mechanisms that regulate its promiscuous binding, we have determined the crystal structure of the IL-10R2 ectodomain at 2.14 A resolution. IL-10R2 residues required for binding were identified by alanine scanning and used to derive computational models of IL-10/IL-10R1/IL-10R2 and IL-22/IL-22R1/IL-10R2 ternary complexes. The models reveal a conserved binding epitope that is surrounded by two clefts that accommodate the structural and chemical diversity of the cytokines. These results provide a structural framework for interpreting IL-10R2 single nucleotide polymorphisms associated with human disease.

Organizational Affiliation

Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Macromolecule Content

Total Structure Weight: 48.22 kDa
Atom Count: 3,551
Modeled Residue Count: 397
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-10 receptor subunit beta	A, B	201	Homo sapiens	Mutation(s): 6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08334 (Homo sapiens) Explore Q08334 Go to UniProtKB: Q08334
PHAROS: Q08334 GTEx: ENSG00000243646
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08334
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.239 (Depositor), 0.242 (DCC)
R-Value Work: 0.210 (Depositor), 0.211 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.839	α = 90
b = 124.839	β = 90
c = 84.223	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
SOLVE	phasing
ARP/wARP	model building
CNS	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Yoon, S.I.

Walter, M.R.

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Advisory, Refinement description
Version 1.3: 2018-08-29
Changes: Data collection, Source and taxonomy, Structure summary
Version 1.4: 2021-10-13
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Structure summary