2WWZ | pdb_00002wwz

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.202 (Depositor), 0.202 (DCC)
R-Value Work:
0.178 (Depositor), 0.176 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/nsmb.1731
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CH28
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NYJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.202 (Depositor), 0.202 (DCC)
R-Value Work: 0.178 (Depositor), 0.176 (DCC)
R-Value Observed: 0.179 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Revision History (Full details and data files)

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