9AZJ | pdb_00009azj

Structure of ubiquitinated NEMO UBAN K285C-Ub G76C bound to HOIP NZF1

• PDB DOI: https://doi.org/10.2210/pdb9AZJ/pdb

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


• Deposited: 2024-03-11 Released: 2024-07-31 
• Deposition Author(s): Michel, M.A., Scutts, S., Komander, D.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), National Health and Medical Research Council (NHMRC, Australia), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 
  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Structure of TAB2 NZF domain bound to K6 / Lys6-linked diubiquitin

Michel, M.A., Scutts, S., Komander, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A4B3C2 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.

Macromolecule Content 

• Total Structure Weight: 83.06 kDa 
• Atom Count: 4,258 
• Modeled Residue Count: 589 
• Deposited Residue Count: 718 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NF-kappa-B essential modulator	A, B, C, D	108	Homo sapiens	Mutation(s): 1  Gene Names: IKBKG, FIP3, NEMO
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K9 (Homo sapiens) Explore Q9Y6K9  Go to UniProtKB:  Q9Y6K9
PHAROS:  Q9Y6K9 GTEx:  ENSG00000269335

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF31	E, G	29	Homo sapiens	Mutation(s): 0  Gene Names: RNF31, ZIBRA EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EP0 (Homo sapiens) Explore Q96EP0  Go to UniProtKB:  Q96EP0
PHAROS:  Q96EP0 GTEx:  ENSG00000092098

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	F, H [auth S], I [auth Z]	76	Homo sapiens	Mutation(s): 1  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
ZN	J [auth E], K [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free:  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.828	α = 90
b = 101.447	β = 90
c = 144.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Michel, M.A., Scutts, S., Komander, D.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	U105192732
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1178122
European Research Council (ERC)	European Union	724804

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary