PDBsum entry 3fx0

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protein Protein-protein interface(s) links
Signaling protein PDB id
Protein chains
63 a.a. *
71 a.a. *
* Residue conservation analysis
PDB id:
Name: Signaling protein
Title: Crystal structure of human nemo cc2_lz domain
Structure: Nf-kappa-b essential modulator. Chain: a, b. Fragment: cc2_lz domain. Synonym: nemo, nf-kappa-b essential modifier, inhibitor of nuclear factor kappa-b kinase subunit gamma, ikb kinase subunit gamma, i-kappa-b kinase gamma, ikk-gamma, ikkg, ikb kinase-associated protein 1, ikkap1, fip-3. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ikbkg, fip3, nemo. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.20Å     R-factor:   0.247     R-free:   0.306
Authors: Y.C.Lo,S.C.Lin,H.Wu
Key ref:
Y.C.Lo et al. (2009). Structural basis for recognition of diubiquitins by NEMO. Mol Cell, 33, 602-615. PubMed id: 19185524 DOI: 10.1016/j.molcel.2009.01.012
19-Jan-09     Release date:   07-Apr-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9Y6K9  (NEMO_HUMAN) -  NF-kappa-B essential modulator
419 a.a.
63 a.a.
Protein chain
Pfam   ArchSchema ?
Q9Y6K9  (NEMO_HUMAN) -  NF-kappa-B essential modulator
419 a.a.
71 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure


DOI no: 10.1016/j.molcel.2009.01.012 Mol Cell 33:602-615 (2009)
PubMed id: 19185524  
Structural basis for recognition of diubiquitins by NEMO.
Y.C.Lo, S.C.Lin, C.C.Rospigliosi, D.B.Conze, C.J.Wu, J.D.Ashwell, D.Eliezer, H.Wu.
NEMO is the regulatory subunit of the IkappaB kinase (IKK) in NF-kappaB activation, and its CC2-LZ region interacts with Lys63 (K63)-linked polyubiquitin to recruit IKK to receptor signaling complexes. In vitro, CC2-LZ also interacts with tandem diubiquitin. Here we report the crystal structure of CC2-LZ with two dimeric coiled coils representing CC2 and LZ, respectively. Surprisingly, mutagenesis and nuclear magnetic resonance experiments reveal that the binding sites for diubiquitins at LZ are composites of both chains and that each ubiquitin in diubiquitins interacts with symmetrical NEMO asymmetrically. For tandem diubiquitin, the first ubiquitin uses the conserved hydrophobic patch and the C-terminal tail, while the second ubiquitin uses an adjacent surface patch. For K63-linked diubiquitin, the proximal ubiquitin uses its conserved hydrophobic patch, while the distal ubiquitin mostly employs the C-terminal arm including the K63 linkage residue. These studies uncover the energetics and geometry for mutual recognition of NEMO and diubiquitins.
  Selected figure(s)  
Figure 4.
Figure 4. Mapped Ub-Binding Site of NEMO
(A) NEMO residues that are important for tandem and K63-linked di-Ub interaction are shown in the stereo ribbon diagram of the CC2-LZ structure. Residues labeled in the red shades caused most drastic effects when mutated. Those labeled in the cyan shades caused less drastic effects. R319 is shown in yellow to indicate that it is involved in tandem, but not K63-linked, di-Ub binding.
(B) The same residues are shown on a surface representation of the structure. Residues from one chain are labeled on the right, and residues from the other chain are labeled on the left of the structure. The ovals at the right panel indicate the two separate symmetrical Ub-binding sites.
(C) The electrostatic surface representation of CC2-LZ.
Figure 7.
Figure 7. Model of NEMO:Di-Ub Interactions
(A) The NEMO:K63-linked di-Ub interaction model produced by HADDOCK. Only the LZ region of NEMO dimer is shown in blue and magenta for each chain, respectively. The distal and the proximal Ub molecules are in green and cyan, respectively. Residues critical for NEMO interaction are labeled and shown in red. Those that are less critical for NEMO interaction are shown in pink, but not labeled.
(B) Same as (A), but rotated approximately 90° around the horizontal axis. The critical interaction patches are circled by ovals.
(C) The NEMO:tandem di-Ub interaction model produced by HADDOCK. Only the LZ region of NEMO dimer is shown in blue and magenta for each chain, respectively. The first and the second Ub molecules are in green and cyan, respectively. Residues critical for NEMO interaction are labeled and shown in red. Those that are less critical for NEMO interaction are shown in pink, but not labeled.
(D) Same as (C), but rotated approximately 90° around the horizontal axis. The critical interaction patches are circled by ovals.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 33, 602-615) copyright 2009.  
  Figures were selected by an automated process.  

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.  
21455173 B.Gerlach, S.M.Cordier, A.C.Schmukle, C.H.Emmerich, E.Rieser, T.L.Haas, A.I.Webb, J.A.Rickard, H.Anderton, W.W.Wong, U.Nachbur, L.Gangoda, U.Warnken, A.W.Purcell, J.Silke, and H.Walczak (2011).
Linear ubiquitination prevents inflammation and regulates immune signalling.
  Nature, 471, 591-596.  
21448225 C.Grabbe, K.Husnjak, and I.Dikic (2011).
The spatial and temporal organization of ubiquitin networks.
  Nat Rev Mol Cell Biol, 12, 295-307.  
21135870 C.Zheng, Q.Yin, and H.Wu (2011).
Structural studies of NF-κB signaling.
  Cell Res, 21, 183-195.  
21423167 G.Xu, Y.C.Lo, Q.Li, G.Napolitano, X.Wu, X.Jiang, M.Dreano, M.Karin, and H.Wu (2011).
Crystal structure of inhibitor of κB kinase β.
  Nature, 472, 325-330.
PDB codes: 3qa8 3qad 3rzf
21138416 K.Clark, M.Peggie, L.Plater, R.J.Sorcek, E.R.Young, J.B.Madwed, J.Hough, E.G.McIver, and P.Cohen (2011).
Novel cross-talk within the IKK family controls innate immunity.
  Biochem J, 434, 93.  
21135871 S.Liu, and Z.J.Chen (2011).
Expanding role of ubiquitination in NF-κB signaling.
  Cell Res, 21, 6.  
21187855 S.Miyamoto (2011).
Nuclear initiated NF-κB signaling: NEMO and ATM take center stage.
  Cell Res, 21, 116-130.  
20923877 D.Boehm, B.E.Gewurz, E.Kieff, and E.Cahir-McFarland (2010).
Epstein-Barr latent membrane protein 1 transformation site 2 activates NF-kappaB in the absence of NF-kappaB essential modifier residues 133-224 or 373-419.
  Proc Natl Acad Sci U S A, 107, 18103-18108.  
21111228 F.Ikeda, N.Crosetto, and I.Dikic (2010).
What determines the specificity and outcomes of ubiquitin signaling?
  Cell, 143, 677-681.  
20181483 F.Liu, and K.J.Walters (2010).
Multitasking with ubiquitin through multivalent interactions.
  Trends Biochem Sci, 35, 352-360.  
  21113390 H.Habelhah (2010).
Emerging complexity of protein ubiquitination in the NF-κB pathway.
  Genes Cancer, 1, 735-747.  
  20357899 H.Wu, Y.C.Lo, and S.C.Lin (2010).
Recent advances in polyubiquitin chain recognition.
  F1000 Biol Rep, 2, 1-5.  
21095585 I.Bosanac, I.E.Wertz, B.Pan, C.Yu, S.Kusam, C.Lam, L.Phu, Q.Phung, B.Maurer, D.Arnott, D.S.Kirkpatrick, V.M.Dixit, and S.G.Hymowitz (2010).
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.
  Mol Cell, 40, 548-557.
PDB codes: 3oj3 3oj4
  20300215 I.E.Wertz, and V.M.Dixit (2010).
Signaling to NF-kappaB: regulation by ubiquitination.
  Cold Spring Harb Perspect Biol, 2, a003350.  
20529958 J.Gautheron, A.Pescatore, F.Fusco, E.Esposito, S.Yamaoka, F.Agou, M.V.Ursini, and G.Courtois (2010).
Identification of a new NEMO/TRAF6 interface affected in incontinentia pigmenti pathology.
  Hum Mol Genet, 19, 3138-3149.  
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.  
21113135 J.N.Dynek, T.Goncharov, E.C.Dueber, A.V.Fedorova, A.Izrael-Tomasevic, L.Phu, E.Helgason, W.J.Fairbrother, K.Deshayes, D.S.Kirkpatrick, and D.Vucic (2010).
c-IAP1 and UbcH5 promote K11-linked polyubiquitination of RIP1 in TNF signalling.
  EMBO J, 29, 4198-4209.  
19680262 J.Silke, and R.Brink (2010).
Regulation of TNFRSF and innate immune signalling complexes by TRAFs and cIAPs.
  Cell Death Differ, 17, 35-45.  
20404851 T.Kawai, and S.Akira (2010).
The role of pattern-recognition receptors in innate immunity: update on Toll-like receptors.
  Nat Immunol, 11, 373-384.  
19927158 W.W.Wong, I.E.Gentle, U.Nachbur, H.Anderton, D.L.Vaux, and J.Silke (2010).
RIPK1 is not essential for TNFR1-induced activation of NF-kappaB.
  Cell Death Differ, 17, 482-487.  
20932476 Z.H.Wu, E.T.Wong, Y.Shi, J.Niu, Z.Chen, S.Miyamoto, and V.Tergaonkar (2010).
ATM- and NEMO-dependent ELKS ubiquitination coordinates TAK1-mediated IKK activation in response to genotoxic stress.
  Mol Cell, 40, 75-86.  
19858201 A.D.Jacobson, N.Y.Zhang, P.Xu, K.J.Han, S.Noone, J.Peng, and C.W.Liu (2009).
The lysine 48 and lysine 63 ubiquitin conjugates are processed differently by the 26 s proteasome.
  J Biol Chem, 284, 35485-35494.  
19763089 E.Laplantine, E.Fontan, J.Chiaravalli, T.Lopez, G.Lakisic, M.Véron, F.Agou, and A.Israël (2009).
NEMO specifically recognizes K63-linked poly-ubiquitin chains through a new bipartite ubiquitin-binding domain.
  EMBO J, 28, 2885-2895.  
19422324 F.J.Ivins, M.G.Montgomery, S.J.Smith, A.C.Morris-Davies, I.A.Taylor, and K.Rittinger (2009).
NEMO oligomerization and its ubiquitin-binding properties.
  Biochem J, 421, 243-251.  
19404332 F.Randow, and P.J.Lehner (2009).
Viral avoidance and exploitation of the ubiquitin system.
  Nat Cell Biol, 11, 527-534.  
19773779 I.Dikic, S.Wakatsuki, and K.J.Walters (2009).
Ubiquitin-binding domains - from structures to functions.
  Nat Rev Mol Cell Biol, 10, 659-671.  
19956206 I.Dikic, and V.Dötsch (2009).
Ubiquitin linkages make a difference.
  Nat Struct Mol Biol, 16, 1209-1210.  
19620964 J.J.Sims, A.Haririnia, B.C.Dickinson, D.Fushman, and R.E.Cohen (2009).
Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains.
  Nat Struct Mol Biol, 16, 883-889.  
19543231 K.Iwai, and F.Tokunaga (2009).
Linear polyubiquitination: a new regulator of NF-kappaB activation.
  EMBO Rep, 10, 706-713.  
19627256 S.Carpenter, and L.A.O'Neill (2009).
Recent insights into the structure of Toll-like receptors and post-translational modifications of their associated signalling proteins.
  Biochem J, 422, 1.  
19303852 S.Rahighi, F.Ikeda, M.Kawasaki, M.Akutsu, N.Suzuki, R.Kato, T.Kensche, T.Uejima, S.Bloor, D.Komander, F.Randow, S.Wakatsuki, and I.Dikic (2009).
Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation.
  Cell, 136, 1098-1109.
PDB codes: 2zvn 2zvo 3f89
  20066103 T.Huxford, and G.Ghosh (2009).
A structural guide to proteins of the NF-kappaB signaling module.
  Cold Spring Harbor Perspect Biol, 1, a000075.  
19820708 T.L.Thurston, G.Ryzhakov, S.Bloor, N.von Muhlinen, and F.Randow (2009).
The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria.
  Nat Immunol, 10, 1215-1221.  
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.