6SP3 | pdb_00006sp3

mouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 1

• PDB DOI: https://doi.org/10.2210/pdb6SP3/pdb

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


• Deposited: 2019-08-30 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: 3.00 Å
• R-Value Free: 
  0.267 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7PUR

Literature

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

Bloch, Y., Savvides, S.N.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 80.98 kDa 
• Atom Count: 4,780 
• Modeled Residue Count: 603 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit beta	A, B	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	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	C, D	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.267 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.8	α = 90
b = 176.14	β = 108.963
c = 54.37	γ = 90

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: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary