2WWZ

TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121

• PDB DOI: https://doi.org/10.2210/pdb2WWZ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-30 Released: 2009-11-24 
• Deposition Author(s): Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., Komander, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.202 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

Two-Sided Ubiquitin Binding Explains Specificity of the Tab2 Nzf Domain

Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., Komander, D.

(2009) Nat Struct Mol Biol 16: 1328

• PubMed: 19935683 
• DOI: https://doi.org/10.1038/nsmb.1731
• Primary Citation of Related Structures:  
  2WWZ, 2WX0, 2WX1


• PubMed Abstract: 
  

  The protein kinase TAK1 is activated by binding to Lys63 (K63)-linked ubiquitin chains through its subunit TAB2. Here we analyze crystal structures of the TAB2 NZF domain bound to Lys63-linked di- and triubiquitin, revealing that TAB2 binds adjacent ubiquitin moieties via two distinct binding sites. The conformational constraints imposed by TAB2 on a Lys63 dimer cannot be adopted by linear chains, explaining why TAK1 cannot be activated by linear ubiquitination events.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 20.96 kDa 
• Atom Count: 1,726 
• Modelled Residue Count: 180 
• Deposited Residue Count: 184 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN	A, B	76	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7-INTERACTING PROTEIN 2	C	32	Homo sapiens	Mutation(s): 0
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.202 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.98	α = 90
b = 69.61	β = 90
c = 71.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Kulathu, Y., Akutsu, M., Bremm, A., Hofmann, K., Komander, D.

Revision History  

• Version 1.0: 2009-11-24
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-31
  Changes: Advisory, Data collection, Derived calculations
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other