8T48

The N4BP1 CUE-like domain in complex with linear di-Ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb8T48/pdb

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


• Deposited: 2023-06-08 Released: 2024-03-13 
• Deposition Author(s): Schubert, A.F., Harris, S.F.
• Funding Organization(s): F. Hoffmann-La Roche LTD

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 

Literature

N4BP1 coordinates IKK family crosstalk to limit inflammation

Gitlin, A.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 54.18 kDa 
• Atom Count: 4,022 
• Modelled Residue Count: 418 
• Deposited Residue Count: 480 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Di-Ubiquitin	A, B	172	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD4-binding protein 1	C, D	68	Homo sapiens	Mutation(s): 1  Gene Names: N4BP1, KIAA0615 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75113 (Homo sapiens) Explore O75113  Go to UniProtKB:  O75113
PHAROS:  O75113 GTEx:  ENSG00000102921

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
LI	F [auth B]	LITHIUM ION Li HBBGRARXTFLTSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.789	α = 90
b = 118.716	β = 91.72
c = 50.695	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Schubert, A.F., Harris, S.F.

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Funding Organization	Location	Grant Number
F. Hoffmann-La Roche LTD	Switzerland	--

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release