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PDBsum entry 3jsv
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protein Protein-protein interface(s) links
Signaling protein/transcription PDB id
3jsv

 

 

 

 

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Contents
Protein chains
76 a.a. *
77 a.a. *
83 a.a. *
Waters ×26
* Residue conservation analysis
PDB id:
3jsv
Name: Signaling protein/transcription
Title: Crystal structure of mouse nemo cozi in complex with lys63-linked di- ubiquitin
Structure: Ubiquitin. Chain: a. Engineered: yes. Mutation: yes. Ubiquitin. Chain: b. Engineered: yes. Mutation: yes. Nf-kappa-b essential modulator.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. Mouse. Organism_taxid: 10090. Gene: ikbkg, nemo, nemo(249-343).
Resolution:
2.70Å     R-factor:   0.250     R-free:   0.294
Authors: A.Yoshikawa,Y.Sato,H.Mimura,M.Yamashita,A.Yamagata,S.Fukai
Key ref: A.Yoshikawa et al. (2009). Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin. Febs Lett, 583, 3317-3322. PubMed id: 19766637
Date:
11-Sep-09     Release date:   27-Oct-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		685 a.a.
76 a.a.*
Protein chain
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		685 a.a.
77 a.a.*
Protein chains
Pfam   ArchSchema ?
O88522  (NEMO_MOUSE) -  NF-kappa-B essential modulator from Mus musculus
Seq:
Struc: 		412 a.a.
83 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 

 
Febs Lett 583:3317-3322 (2009)
PubMed id: 19766637  
 
 
Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin.
A.Yoshikawa, Y.Sato, M.Yamashita, H.Mimura, A.Yamagata, S.Fukai.
 
  ABSTRACT  
 
NEMO is essential for activation of the NF-kappaB signaling pathway, which is regulated by ubiquitination of proteins. The C-terminal leucine zipper of NEMO and its adjacent coiled-coil region (CC2-LZ) reportedly bind to linear ubiquitin chains with 1 microM affinity and to Lys 63-linked chains with 100 microM affinity. Here we report the crystal structure of the CC2-LZ region of mouse NEMO in complex with Lys 63-linked di-ubiquitin (K63-Ub(2)) at 2.7A resolution. The ubiquitin-binding region consists of a 130A-long helix and forms a parallel coiled-coil dimer. The Ile 44-centered hydrophobic patch of ubiquitin is recognized in the middle of the NEMO ubiquitin-binding region. NEMO interacts with each K63-Ub(2)via a single ubiquitin-binding site, consistent with low affinity binding with K63-Ub(2).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22820888 Y.Kulathu, and D.Komander (2012).
Atypical ubiquitylation - the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages.
  Nat Rev Mol Cell Biol, 13, 508-523.  
21540891 C.Behrends, and J.W.Harper (2011).
Constructing and decoding unconventional ubiquitin chains.
  Nat Struct Mol Biol, 18, 520-528.  
21135870 C.Zheng, Q.Yin, and H.Wu (2011).
Structural studies of NF-κB signaling.
  Cell Res, 21, 183-195.  
21187855 S.Miyamoto (2011).
Nuclear initiated NF-κB signaling: NEMO and ATM take center stage.
  Cell Res, 21, 116-130.  
20181483 F.Liu, and K.J.Walters (2010).
Multitasking with ubiquitin through multivalent interactions.
  Trends Biochem Sci, 35, 352-360.  
  20357899 H.Wu, Y.C.Lo, and S.C.Lin (2010).
Recent advances in polyubiquitin chain recognition.
  F1000 Biol Rep, 2, 1-5.  
20502939 J.Gautheron, and G.Courtois (2010).
"Without Ub I am nothing": NEMO as a multifunctional player in ubiquitin-mediated control of NF-kappaB activation.
  Cell Mol Life Sci, 67, 3101-3113.  
19935683 Y.Kulathu, M.Akutsu, A.Bremm, K.Hofmann, and D.Komander (2009).
Two-sided ubiquitin binding explains specificity of the TAB2 NZF domain.
  Nat Struct Mol Biol, 16, 1328-1330.
PDB codes: 2wwz 2wx0 2wx1
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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