7PUR | pdb_00007pur

mouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 2

• PDB DOI: https://doi.org/10.2210/pdb7PUR/pdb

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


• Deposited: 2021-09-30 Released: 2021-11-10 
• Deposition Author(s): Bloch, Y., Savvides, S.N.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free: 
  0.324 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.285 (Depositor) 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6sp3

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 81.11 kDa 
• Atom Count: 4,708 
• Modeled Residue Count: 594 
• 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	3D 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	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	D	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL GlyCosmos:  G55220VL GlyGen:  G55220VL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.90 Å
• R-Value Free:  0.324 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.285 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.263	α = 90
b = 158.334	β = 100.214
c = 68.552	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Bloch, Y., Savvides, S.N.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	--

Revision History  

• Version 1.0: 2021-11-10
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary