Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.24 kDa 
• Atom Count: 7197 
• Modelled Residue Count: 851 
• Deposited Residue Count: 852 
• Unique protein chains: 1

1YKB

Crystal Structure of Insect Cell Expressed IL-22

• DOI: 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.232 

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 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Interleukin-22)	A, B, C, D, E, F	142	Homo sapiens	Mutation(s): 0  Gene Names: IL22, ILTIF, ZCYTO18, UNQ3099/PRO10096
Find proteins for Q9GZX6 (Homo sapiens) Explore Q9GZX6  Go to UniProtKB:  Q9GZX6
NIH Common Fund Data Resources
PHAROS:  Q9GZX6 GTEx:  ENSG00000127318

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, J, K, L	2		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.265 
• R-Value Work: 0.232 
• 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

Entry History 

Deposition Data

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

Revision History  

• 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