1F42 | pdb_00001f42

THE P40 DOMAIN OF HUMAN INTERLEUKIN-12

• PDB DOI: https://doi.org/10.2210/pdb1F42/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2000-06-07 Released: 2001-06-13 
• Deposition Author(s): Yoon, C., Johnston, S.C., Tang, J., Tobin, J.F., Somers, W.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.281 (Depositor) 
• R-Value Work: 
  0.227 (Depositor) 
• R-Value Observed: 
  0.281 (Depositor) 

Literature

Charged residues dominate a unique interlocking topography in the heterodimeric cytokine interleukin-12.

Yoon, C., Johnston, S.C., Tang, J., Stahl, M., Tobin, J.F., Somers, W.S.

(2000) EMBO J 19: 3530-3541

• PubMed: 10899108 
• DOI: https://doi.org/10.1093/emboj/19.14.3530
• Primary Citation Related Structures: 
  1F42, 1F45


• PubMed Abstract: 
  

  Human interleukin-12 (IL-12, p70) is an early pro-inflammatory cytokine, comprising two disulfide-linked subunits, p35 and p40. We solved the crystal structures of monomeric human p40 at 2.5 A and the human p70 complex at 2.8 A resolution, which reveals that IL-12 is similar to class 1 cytokine-receptor complexes. They also include the first description of an N-terminal immunoglobulin-like domain, found on the p40 subunit. Several charged residues from p35 and p40 intercalate to form a unique interlocking topography, shown by mutagenesis to be critical for p70 formation. A central arginine residue from p35 projects into a deep pocket on p40, which may be an ideal target for a small molecule antagonist of IL-12 formation.

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Organizational Affiliation: 
• Departments of Musculoskeletal Sciences and Biological Chemistry, Wyeth Research, 87 Cambridge Park Drive, Cambridge, MA 02140, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.72 kDa 
• Atom Count: 2,456 
• Modeled Residue Count: 297 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTERLEUKIN-12 BETA CHAIN	A	306	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P29460 (Homo sapiens) Explore P29460  Go to UniProtKB:  P29460
PHAROS:  P29460 GTEx:  ENSG00000113302
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P29460-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNB	C [auth A], D [auth A]	5-MERCAPTO-2-NITRO-BENZOIC ACID C7 H5 N O4 S GANZODCWZFAEGN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.281 (Depositor) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34	α = 90
b = 55	β = 90
c = 189.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-06-13 
Deposition Author(s): Yoon, C., Johnston, S.C., Tang, J., Tobin, J.F., Somers, W.S.

Revision History  

• Version 1.0: 2001-06-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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: 2024-10-09
  Changes: Advisory, Data collection, Database references, Structure summary