Macromolecule Content

• Total Structure Weight: 28.98 kDa 
• Atom Count: 2027 
• Residue Count: 263 
• Unique protein chains: 2

2KDF

NMR structure of minor S5a (196-306):K48 linked diubiquitin species

• DOI: 10.2210/pdb2KDF/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-06 Released: 2009-09-01 
• Deposition Author(s): Zhang, N., Wang, Q., Ehlinger, A., Randles, L., Lary, J.W., Kang, Y., Haririnia, A., Cole, J.L., Fushman, D., Walters, K.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 7 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.

Zhang, N., Wang, Q., Ehlinger, A., Randles, L., Lary, J.W., Kang, Y., Haririnia, A., Storaska, A.J., Cole, J.L., Fushman, D., Walters, K.J.

(2009) Mol Cell 35: 280-290

• PubMed: 19683493 
• DOI: 10.1016/j.molcel.2009.06.010
• Primary Citation of Related Structures:  
  2KDF, 2KDE


• PubMed Abstract: 
  

Degradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the "proximal" one) is covalently bonded to G76 of the other (the "distal" subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	A	111	Homo sapiens	Mutation(s): 0  Gene Names: PSMD4, MCB1
Find proteins for P55036 (Homo sapiens) Explore P55036  Go to UniProtKB:  P55036
NIH Common Fund Data Resources
PHAROS  P55036 GTEx  ENSG00000159352

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 7 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KDF Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-06 
• Released Date: 2009-09-01 
Deposition Author(s): Zhang, N., Wang, Q., Ehlinger, A., Randles, L., Lary, J.W., Kang, Y., Haririnia, A., Cole, J.L., Fushman, D., Walters, K.J.

Revision History 

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance