6SMC | pdb_00006smc

mouse Interleukin-12 subunit beta - p80 homodimer in space group P1

• PDB DOI: https://doi.org/10.2210/pdb6SMC/pdb

• Classification: CYTOKINE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-08-21 Released: 2020-09-09 
• Deposition Author(s): Bloch, Y., Savvides, S.N.
• Funding Organization(s): Research Foundation - Flanders

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.310 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.279 (Depositor), 0.290 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

Starting Model: experimental

Literature

Around she goes: the structure of mouse Interleukin-12 p80

Bloch, Y., Savvides, S.N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS, light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 160.66 kDa 
• Atom Count: 9,784 
• Modeled Residue Count: 1,205 
• Deposited Residue Count: 1,376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit beta	A, B, C, D	344	Mus musculus	Mutation(s): 0  Gene Names: Il12b
UniProt & NIH Common Fund Data Resources
Find proteins for P43432 (Mus musculus) Explore P43432  Go to UniProtKB:  P43432
IMPC:  MGI:96540
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P43432-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	I [auth B], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.310 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.279 (Depositor), 0.290 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.074	α = 68.586
b = 96.791	β = 76.842
c = 107.78	γ = 85.827

Software Package:

Software Name	Purpose
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Bloch, Y., Savvides, S.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	12S0519N
Research Foundation - Flanders	Belgium	G0B4918N
Research Foundation - Flanders	Belgium	G0E1516N

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2022-02-02
  Changes: Database references, Experimental preparation
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary