PDBsum entry 1f9j

Go to PDB code: 
protein Protein-protein interface(s) links
Chaperone PDB id
Protein chains
76 a.a. *
* Residue conservation analysis
PDB id:
Name: Chaperone
Title: Structure of a new crystal form of tetraubiquitin
Structure: Tetraubiquitin. Chain: a, b. Synonym: ubiquitin. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
2.70Å     R-factor:   0.225     R-free:   0.292
Authors: C.L.Phillips,J.Thrower,C.M.Pickart,C.P.Hill
Key ref:
C.L.Phillips et al. (2001). Structure of a new crystal form of tetraubiquitin. Acta Crystallogr D Biol Crystallogr, 57, 341-344. PubMed id: 11173499 DOI: 10.1107/S090744490001800X
10-Jul-00     Release date:   07-Feb-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C
685 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1107/S090744490001800X Acta Crystallogr D Biol Crystallogr 57:341-344 (2001)
PubMed id: 11173499  
Structure of a new crystal form of tetraubiquitin.
C.L.Phillips, J.Thrower, C.M.Pickart, C.P.Hill.
Polyubiquitin chains, in which the C-terminus and a lysine side chain of successive ubiquitin molecules are linked by an isopeptide bond, function to target substrate proteins for degradation by the 26S proteasome. Chains of at least four ubiquitin moieties appear to be required for efficient recognition by the 26S proteasome, although the conformations of the polyubiquitin chains recognized by the proteasome or by other enzymes involved in ubiquitin metabolism are currently unknown. A new crystal form of tetraubiquitin, which has two possible chain connectivities that are indistinguishable in the crystal, is reported. In one possible connectivity, the tetraubiquitin chain is extended and packs closely against the antiparallel neighbor chain in the crystal to conceal a hydrophobic surface implicated in 26S proteasome recognition. In the second possibility, the tetraubiqutitin forms a closed compact structure, in which that same hydrophobic surface is buried. Both of these conformations are quite unlike the structure of tetraubiquitin that was previously determined in a different crystal form [Cook et al. (1994), J. Mol. Biol. 236, 601--609]. The new structure suggests that polyubiquitin chains may possess a substantially greater degree of conformational flexibility than has previously been appreciated.
  Selected figure(s)  
Figure 1.
Figure 1 The flexible linkages between ubiquitin moieties. Superposition of the first ubiquitin moiety of each of the three polyubiquitin crystal structures reveals each of the second ubiquitin moieties to be in a different position. The Ub[4]-2 dimer is shown in red, the Ub[4]-1 dimer in green and the Ub[2] dimer in blue. In each case, the Gly76-Lys148 linkage is shown in CPK representation. The N- and C-termini of the second ubiquitin moiety in each structure are labeled. Figures were created using MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 341-344) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19853612 D.Fushman, and O.Walker (2010).
Exploring the linkage dependence of polyubiquitin conformations using molecular modeling.
  J Mol Biol, 395, 803-814.  
  20357899 H.Wu, Y.C.Lo, and S.C.Lin (2010).
Recent advances in polyubiquitin chain recognition.
  F1000 Biol Reports, 2, 1-5.  
  20823512 J.F.Trempe, N.R.Brown, M.E.Noble, and J.A.Endicott (2010).
A new crystal form of Lys48-linked diubiquitin.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 994-998.
PDB code: 3m3j
19243136 F.E.Reyes-Turcu, and K.D.Wilkinson (2009).
Polyubiquitin binding and disassembly by deubiquitinating enzymes.
  Chem Rev, 109, 1495-1508.  
19489724 F.E.Reyes-Turcu, K.H.Ventii, and K.D.Wilkinson (2009).
Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes.
  Annu Rev Biochem, 78, 363-397.  
20003470 I.A.Qureshi, F.Ferron, C.C.Seh, P.Cheung, and J.Lescar (2009).
Crystallographic structure of ubiquitin in complex with cadmium ions.
  BMC Res Notes, 2, 251.
PDB code: 3h1u
19541633 S.Garcia-Manyes, L.Dougan, and J.M.Fernández (2009).
Osmolyte-induced separation of the mechanical folding phases of ubiquitin.
  Proc Natl Acad Sci U S A, 106, 10540-10545.  
19948475 T.E.Messick, and R.A.Greenberg (2009).
The ubiquitin landscape at DNA double-strand breaks.
  J Cell Biol, 187, 319-326.  
18482987 F.E.Reyes-Turcu, J.R.Shanks, D.Komander, and K.D.Wilkinson (2008).
Recognition of polyubiquitin isoforms by the multiple ubiquitin binding modules of isopeptidase T.
  J Biol Chem, 283, 19581-19592.  
18438605 W.Li, and Y.Ye (2008).
Polyubiquitin chains: functions, structures, and mechanisms.
  Cell Mol Life Sci, 65, 2397-2406.  
17355622 T.Woelk, S.Sigismund, L.Penengo, and S.Polo (2007).
The ubiquitination code: a signalling problem.
  Cell Div, 2, 11.  
16564012 F.E.Reyes-Turcu, J.R.Horton, J.E.Mullally, A.Heroux, X.Cheng, and K.D.Wilkinson (2006).
The ubiquitin binding domain ZnF UBP recognizes the C-terminal diglycine motif of unanchored ubiquitin.
  Cell, 124, 1197-1208.
PDB codes: 2g43 2g45
17114057 M.D.Petroski, G.Kleiger, and R.J.Deshaies (2006).
Evaluation of a diffusion-driven mechanism for substrate ubiquitination by the SCF-Cdc34 ubiquitin ligase complex.
  Mol Cell, 24, 523-534.  
15937902 A.D.van Dijk, D.Fushman, and A.M.Bonvin (2005).
Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
  Proteins, 60, 367-381.
PDB code: 2bgf
15723079 A.Pichler, P.Knipscheer, E.Oberhofer, W.J.van Dijk, R.Körner, J.V.Olsen, S.Jentsch, F.Melchior, and T.K.Sixma (2005).
SUMO modification of the ubiquitin-conjugating enzyme E2-25K.
  Nat Struct Mol Biol, 12, 264-269.
PDB codes: 2bep 2bf8
15556404 C.M.Pickart, and D.Fushman (2004).
Polyubiquitin chains: polymeric protein signals.
  Curr Opin Chem Biol, 8, 610-616.  
14707125 T.D.Mueller, M.Kamionka, and J.Feigon (2004).
Specificity of the interaction between ubiquitin-associated domains and ubiquitin.
  J Biol Chem, 279, 11926-11936.  
15461659 T.Tenno, K.Fujiwara, H.Tochio, K.Iwai, E.H.Morita, H.Hayashi, S.Murata, H.Hiroaki, M.Sato, K.Tanaka, and M.Shirakawa (2004).
Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains.
  Genes Cells, 9, 865-875.  
15479240 W.C.Huang, T.P.Ko, S.S.Li, and A.H.Wang (2004).
Crystal structures of the human SUMO-2 protein at 1.6 A and 1.2 A resolution: implication on the functional differences of SUMO proteins.
  Eur J Biochem, 271, 4114-4122.
PDB codes: 1wm2 1wm3
12832454 K.S.Ryu, K.J.Lee, S.H.Bae, B.K.Kim, K.A.Kim, and B.S.Choi (2003).
Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a.
  J Biol Chem, 278, 36621-36627.
PDB code: 1p1a
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.