1LK3 | pdb_00001lk3

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00791-8
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22301
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01835
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20759
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.240 (Depositor), 0.239 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.187 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2002-07-17

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-11-13
Changes: Advisory, Data collection, Database references, Structure summary