PDBsum entry 3hct

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protein metals Protein-protein interface(s) links
Signaling protein/ligase PDB id
Protein chains
104 a.a. *
148 a.a. *
_ZN ×3
Waters ×195
* Residue conservation analysis
PDB id:
Name: Signaling protein/ligase
Title: Crystal structure of traf6 in complex with ubc13 in the p1 space group
Structure: Tnf receptor-associated factor 6. Chain: a. Fragment: ring and zinc finger 1: unp residues 50-159. Synonym: interleukin-1 signal transducer, ring finger protein 85. Engineered: yes. Ubiquitin-conjugating enzyme e2 n. Chain: b. Synonym: ubiquitin-protein ligase n, ubiquitin carrier
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rnf85, traf6. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: blu, ube2n.
2.10Å     R-factor:   0.212     R-free:   0.278
Authors: Q.Yin,S.-C.Lin,B.Lamothe,M.Lu,Y.-C.Lo,G.Hura,L.Zheng, R.L.Rich,A.D.Campos,D.G.Myszka,M.J.Lenardo,B.G.Darnay,H.Wu
Key ref:
Q.Yin et al. (2009). E2 interaction and dimerization in the crystal structure of TRAF6. Nat Struct Biol, 16, 658-666. PubMed id: 19465916 DOI: 10.1038/nsmb.1605
06-May-09     Release date:   26-May-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9Y4K3  (TRAF6_HUMAN) -  TNF receptor-associated factor 6
522 a.a.
104 a.a.
Protein chain
Pfam   ArchSchema ?
P61088  (UBE2N_HUMAN) -  Ubiquitin-conjugating enzyme E2 N
152 a.a.
148 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: E.C.  - Ubiquitin--protein ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine
+ ubiquitin
+ protein lysine
+ diphosphate
+ protein N-ubiquityllysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     UBC13-UEV1A complex   8 terms 
  Biological process     nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway   44 terms 
  Biochemical function     signal transducer activity     11 terms  


DOI no: 10.1038/nsmb.1605 Nat Struct Biol 16:658-666 (2009)
PubMed id: 19465916  
E2 interaction and dimerization in the crystal structure of TRAF6.
Q.Yin, S.C.Lin, B.Lamothe, M.Lu, Y.C.Lo, G.Hura, L.Zheng, R.L.Rich, A.D.Campos, D.G.Myszka, M.J.Lenardo, B.G.Darnay, H.Wu.
Tumor necrosis factor (TNF) receptor-associated factor (TRAF)-6 mediates Lys63-linked polyubiquitination for NF-kappaB activation via its N-terminal RING and zinc finger domains. Here we report the crystal structures of TRAF6 and its complex with the ubiquitin-conjugating enzyme (E2) Ubc13. The RING and zinc fingers of TRAF6 assume a rigid, elongated structure. Interaction of TRAF6 with Ubc13 involves direct contacts of the RING and the preceding residues, and the first zinc finger has a structural role. Unexpectedly, this region of TRAF6 is dimeric both in the crystal and in solution, different from the trimeric C-terminal TRAF domain. Structure-based mutagenesis reveals that TRAF6 dimerization is crucial for polyubiquitin synthesis and autoubiquitination. Fluorescence resonance energy transfer analysis shows that TRAF6 dimerization induces higher-order oligomerization of full-length TRAF6. The mismatch of dimeric and trimeric symmetry may provide a mode of infinite oligomerization that facilitates ligand-dependent signal transduction of many immune receptors.
  Selected figure(s)  
Figure 2.
(a) Ribbon diagram of the TRAF6 RZ[1]-Ubc13 complex. The Z[2] and Z[3] domains are modeled based on superposition of the TRAF6 RZ[1]–Ubc13 complex with the TRAF6 RZ[123] structure and are shown in gray. (b) Detailed interaction between TRAF6 and Ubc13. TRAF6 is shown in magenta with the carbon atoms of its side chains in yellow. Ubc13 is shown in orange with the carbon atoms of its side chains in gray. (c) Superimposed gel filtration profiles of Ubc13 mixed with wild-type (WT) or mutant TRAF6 RZ[123] designed to disrupt the interaction. Approximate elution positions of molecular weight standards are shown. (d) Yeast two-hybrid experiments on the interaction between Ubc13 and full-length TRAF2, TRAF3, TRAF5, TRAF6 (positive control) and its RING mutant C70A (negative control). (e) Superimposed gel filtration profiles of Ubc13 mixed with wild-type or mutant TRAF6 RZ[123] with interface residues switched to the corresponding sequences in other TRAFs: I72A (mutation to the corresponding TRAF2 sequence), I72K (TRAF3), I72F (TRAF5), L74H (TRAF3 and TRAF5) and L74R (TRAF2). Approximate elution positions of molecular weight standards are shown. (f) Promotion of polyubiquitin chain synthesis by wild-type and mutant TRAF6 RZ[123] in the presence of the E2 complex Ubc13–Uev1A and E1.
Figure 3.
(a) TRAF6 mutants defective in Ubc13 interaction failed to rescue IL-1–induced TRAF6 autoubiquitination in TRAF6-deficient MEFs. The indicated stable cells lines were treated with IL-1 (1 ng ml^-1) for the indicated times and the clarified lysates were immunoblotted with the indicated antibodies. (b) TRAF6 mutants defective in Ubc13 interaction failed to rescue IL-1–induced IKK activation and I B phosphorylation in Traf6^-/- MEFs. IB, immunoblot; WT, wild type.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 658-666) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22902369 H.Dou, L.Buetow, G.J.Sibbet, K.Cameron, and D.T.Huang (2012).
BIRC7-E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer.
  Nat Struct Mol Biol, 19, 876-883.
PDB code: 4auq
21857666 A.Plechanovová, E.G.Jaffray, S.A.McMahon, K.A.Johnson, I.Navrátilová, J.H.Naismith, and R.T.Hay (2011).
Mechanism of ubiquitylation by dimeric RING ligase RNF4.
  Nat Struct Mol Biol, 18, 1052-1059.
PDB code: 2xeu
21187419 B.K.Ganser-Pornillos, V.Chandrasekaran, O.Pornillos, J.G.Sodroski, W.I.Sundquist, and M.Yeager (2011).
Hexagonal assembly of a restricting TRIM5alpha protein.
  Proc Natl Acad Sci U S A, 108, 534-539.  
21135870 C.Zheng, Q.Yin, and H.Wu (2011).
Structural studies of NF-κB signaling.
  Cell Res, 21, 183-195.  
21345212 L.D.Wilson, J.M.Sackett, B.D.Mieczkowski, A.L.Richie, K.Thoemke, J.N.Rumbley, and T.L.Kroft (2011).
Fertilization in C. elegans requires an intact C-terminal RING finger in sperm protein SPE-42.
  BMC Dev Biol, 11, 10.  
21765416 M.F.Calabrese, D.C.Scott, D.M.Duda, C.R.Grace, I.Kurinov, R.W.Kriwacki, and B.A.Schulman (2011).
A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases.
  Nat Struct Mol Biol, 18, 947-949.
PDB code: 3rtr
21135871 S.Liu, and Z.J.Chen (2011).
Expanding role of ubiquitination in NF-κB signaling.
  Cell Res, 21, 6.  
20154706 A.R.Cole, L.P.Lewis, and H.Walden (2010).
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex.
  Nat Struct Mol Biol, 17, 294-298.
PDB code: 3k1l
20385093 C.Zheng, V.Kabaleeswaran, Y.Wang, G.Cheng, and H.Wu (2010).
Crystal structures of the TRAF2: cIAP2 and the TRAF1: TRAF2: cIAP2 complexes: affinity, specificity, and regulation.
  Mol Cell, 38, 101-113.
PDB codes: 3m06 3m0a 3m0d
20832729 D.C.Scott, J.K.Monda, C.R.Grace, D.M.Duda, R.W.Kriwacki, T.Kurz, and B.A.Schulman (2010).
A dual E3 mechanism for Rub1 ligation to Cdc53.
  Mol Cell, 39, 784-796.
PDB codes: 3o2p 3o2u 3o6b
21158740 D.M.Wenzel, K.E.Stoll, and R.E.Klevit (2010).
E2s: structurally economical and functionally replete.
  Biochem J, 433, 31-42.  
  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.  
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.  
20512936 K.Z.Wang, D.L.Galson, and P.E.Auron (2010).
TRAF6 is autoinhibited by an intramolecular interaction which is counteracted by trans-ubiquitination.
  J Cell Biochem, 110, 763-771.  
20817427 P.D.Mace, and S.J.Riedl (2010).
Molecular cell death platforms and assemblies.
  Curr Opin Cell Biol, 22, 828-836.  
20696396 R.C.Benirschke, J.R.Thompson, Y.Nominé, E.Wasielewski, N.Juranić, S.Macura, S.Hatakeyama, K.I.Nakayama, M.V.Botuyan, and G.Mer (2010).
Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.
  Structure, 18, 955-965.
PDB codes: 2kre 3l1x 3l1y 3l1z
19909372 H.Shinohara, and T.Kurosaki (2009).
Comprehending the complex connection between PKCbeta, TAK1, and IKK in BCR signaling.
  Immunol Rev, 232, 300-318.  
19851286 J.L.Parker, and H.D.Ulrich (2009).
Mechanistic analysis of PCNA poly-ubiquitylation by the ubiquitin protein ligases Rad18 and Rad5.
  EMBO J, 28, 3657-3666.  
19818708 M.Zhuang, M.F.Calabrese, J.Liu, M.B.Waddell, A.Nourse, M.Hammel, D.J.Miller, H.Walden, D.M.Duda, S.N.Seyedin, T.Hoggard, J.W.Harper, K.P.White, and B.A.Schulman (2009).
Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases.
  Mol Cell, 36, 39-50.
PDB codes: 3hqh 3hqi 3hql 3hqm 3hsv 3htm 3hu6 3hve 3ivq 3ivv
19810754 Q.Yin, B.Lamothe, B.G.Darnay, and H.Wu (2009).
Structural basis for the lack of E2 interaction in the RING domain of TRAF2.
  Biochemistry, 48, 10558-10567.
PDB code: 3knv
19851334 Y.Ye, and M.Rape (2009).
Building ubiquitin chains: E2 enzymes at work.
  Nat Rev Mol Cell Biol, 10, 755-764.  
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 code is shown on the right.