1YKB

Crystal Structure of Insect Cell Expressed IL-22

PDB DOI: https://doi.org/10.2210/pdb1YKB/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2005-01-17 Released: 2005-07-12
Deposition Author(s): Xu, T., Logsdon, N.J., Walter, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.232 (Depositor), 0.239 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of insect-cell-derived IL-22.

Xu, T., Logsdon, N.J., Walter, M.R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 942-950

PubMed: 15983417 Search on PubMed
DOI: https://doi.org/10.1107/S0907444905009601
Primary Citation of Related Structures:
1YKB

PubMed Abstract:
The crystal structure of interleukin-22 expressed in Drosophila melanogaster S2 cells (IL-22(Dm)) has been determined at 2.6 A resolution. IL-22(Dm) crystals contain six molecules in the asymmetric unit. Comparison of IL-22(Dm) and IL-22(Ec) (interleukin-22 produced in Escherichia coli) structures reveals that N-linked glycosylation causes only minor structural changes to the cytokine. However, 1-4 A main-chain differences are observed between the six IL-22(Dm) monomers at regions corresponding to the IL-22R1 and IL-10R2 binding sites. The structure of the carbohydrate and the conformational variation of IL22(Dm) provide new insights into IL-22 receptor recognition.

Organizational Affiliation

Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Macromolecule Content

Total Structure Weight: 102.24 kDa
Atom Count: 7,197
Modelled Residue Count: 851
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Interleukin-22)	A, B, C, D, E A, B, C, D, E, F	142	Homo sapiens	Mutation(s): 0 Gene Names: IL22, ILTIF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZX6 (Homo sapiens) Explore Q9GZX6 Go to UniProtKB: Q9GZX6
PHAROS: Q9GZX6 GTEx: ENSG00000127318
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZX6
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F	Go to GlyGen: Q9GZX6-1
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

Help

Entity ID: 2
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	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, J, K, L	2		N-Glycosylation	Interactions Focus chain H Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain H Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-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	5		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G17392HI GlyCosmos: G17392HI GlyGen: G17392HI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth E]	M [auth A], N [auth B], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265 (Depositor), 0.264 (DCC)
R-Value Work: 0.232 (Depositor), 0.239 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.877	α = 90
b = 62.227	β = 91.35
c = 139.524	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
BEAST	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-07-12

Deposition Author(s):

Xu, T.

Logsdon, N.J.

Walter, M.R.

Revision History (Full details and data files)

Version 1.0: 2005-07-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-30
Changes: Data collection, Database references, Structure summary