9AVW | pdb_00009avw

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

• PDB DOI: https://doi.org/10.2210/pdb9AVW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-05 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: 1.75 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (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 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.7 kDa 
• Atom Count: 1,560 
• Modeled Residue Count: 176 
• Deposited Residue Count: 335 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A, B	152	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
TGF-beta-activated kinase 1 and MAP3K7-binding protein 2	C	31	Homo sapiens	Mutation(s): 0  Gene Names: TAB2, KIAA0733, MAP3K7IP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYJ8 (Homo sapiens) Explore Q9NYJ8  Go to UniProtKB:  Q9NYJ8
PHAROS:  Q9NYJ8 GTEx:  ENSG00000055208

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], J [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.663	α = 90
b = 89.663	β = 90
c = 86.12	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	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: 2024-10-30
  Changes: Structure summary