1LK3

ENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT

• PDB DOI: https://doi.org/10.2210/pdb1LK3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-04-23 Released: 2002-07-17 
• Deposition Author(s): Josephson, K., Jones, B.C., Walter, L.J., DiGiacomo, R., Indelicato, S.R., Walter, M.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.240 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 

Literature

Noncompetitive antibody neutralization of IL-10 revealed by protein engineering and x-ray crystallography.

Josephson, K., Jones, B.C., Walter, L.J., DiGiacomo, R., Indelicato, S.R., Walter, M.R.

(2002) Structure 10: 981-987

• PubMed: 12121653 
• DOI: https://doi.org/10.1016/s0969-2126(02)00791-8
• Primary Citation of Related Structures:  
  1LK3


• PubMed Abstract: 
  

  IL-10 is a dimeric cytokine that must engage its high-affinity cell surface receptor, IL-10R1, to induce multiple cellular activities. Here we report the 1.9 A crystal structure of an engineered IL-10 monomer (IL-10M1) in complex with a neutralizing Fab fragment (9D7Fab). 9D7Fab and IL-10R1 bind distinct nonoverlapping surfaces on IL-10M1. Antagonism of the IL-10M1/IL-10R1 interaction is the result of 9D7Fab-induced conformational changes in the CD loop of IL-10M1 that indirectly alter the structure of the IL-10R1 binding site. A single mutation (Ile87Ala) in the same CD loop region of the Epstein-Barr virus IL-10 (ebvIL-10) also reduces IL-10R1 binding affinity, suggesting that ebvIL-10 and 9D7Fab use similar allosteric mechanisms to modulate IL-10R1 affinity and biological activity.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.69 kDa 
• Atom Count: 9,973 
• Modelled Residue Count: 1,130 
• Deposited Residue Count: 1,178 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-10	A, D [auth B]	160	Homo sapiens	Mutation(s): 0  Gene Names: IL10
UniProt & NIH Common Fund Data Resources
Find proteins for P22301 (Homo sapiens) Explore P22301  Go to UniProtKB:  P22301
PHAROS:  P22301 GTEx:  ENSG00000136634

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
9D7 Light Chain	B [auth L], E [auth M]	210	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P01835 (Rattus norvegicus) Explore P01835  Go to UniProtKB:  P01835

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
9D7 Heavy Chain	C [auth H], F [auth I]	219	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P20759 (Rattus norvegicus) Explore P20759  Go to UniProtKB:  P20759

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.240 
• R-Value Work: 0.187 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.554	α = 90
b = 75.616	β = 96.85
c = 111.975	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-17 
Deposition Author(s): Josephson, K., Jones, B.C., Walter, L.J., DiGiacomo, R., Indelicato, S.R., Walter, M.R.

Revision History  

• Version 1.0: 2002-07-17
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance