7NPO

Branched K48-K63-Ub3

• PDB DOI: https://doi.org/10.2210/pdb7NPO/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-02-27 Released: 2022-08-10 
• Deposition Author(s): Lange, S.M., Kwasna, D., Kulathu, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Literature

Branched Lys48-Lys63-linked triubiquitin

Lange, S.M., Kulathu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.55 kDa 
• Atom Count: 1,774 
• Modelled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	72	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, C	76	Homo sapiens	Mutation(s): 2  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.63	α = 90
b = 77.57	β = 123.975
c = 50.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
Aimless	data scaling
PHASER	phasing
MxCuBE	data collection
pointless	data scaling
STARANISO	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Lange, S.M., Kwasna, D., Kulathu, Y.

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description