Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.51 kDa 
• Atom Count: 1529 
• Modelled Residue Count: 188 
• Deposited Residue Count: 228 
• Unique protein chains: 2

2NBV

Solution structure of the Rpn13 Pru domain engaging the hPLIC2 UBL domain

• DOI: 10.2210/pdb2NBV/pdb
• BMRB: 25995

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


• Deposited: 2016-03-12 Released: 2016-07-20 
• Deposition Author(s): Chen, X., Walters, K.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.

Chen, X., Randles, L., Shi, K., Tarasov, S.G., Aihara, H., Walters, K.J.

(2016) Structure 24: 1257-1270

• PubMed: 27396824 
• DOI: 10.1016/j.str.2016.05.018
• Primary Citation of Related Structures:  
  2NBW, 2NBV, 2NBU, 5IRS


• PubMed Abstract: 
  

Three receptors (Rpn1/S2/PSMD2, Rpn10/S5a, Rpn13/Adrm1) in the proteasome bind substrates by interacting with conjugated ubiquitin chains and/or shuttle factors (Rad23/HR23, Dsk2/PLIC/ubiquilin, Ddi1) that carry ubiquitinated substrates to proteasomes. We solved the structure of two such receptors with their preferred shuttle factor, namely hRpn13(Pru):hPLIC2(UBL) and scRpn1 T1:scRad23(UBL). We find that ubiquitin folds in Rad23 and Dsk2 are fine-tuned by residue substitutions to achieve high affinity for Rpn1 and Rpn13, respectively. A single substitution in hPLIC2 yields enhanced interactions with the Rpn13 ubiquitin contact surface and sterically blocks hRpn13 binding to its preferred ubiquitin chain type, K48-linked chains. Rpn1 T1 binds two ubiquitins in tandem and we find that Rad23 binds exclusively to the higher-affinity Helix28/Helix30 site. Rad23 contacts at Helix28/Helix30 are optimized compared to ubiquitin by multiple conservative amino acid substitutions. Thus, shuttle factors deliver substrates to proteasomes through fine-tuned ubiquitin-like surfaces.

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Organizational Affiliation: 

Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasomal ubiquitin receptor ADRM1	A	150	Homo sapiens	Mutation(s): 0  Gene Names: ADRM1, GP110
Find proteins for Q16186 (Homo sapiens) Explore Q16186  Go to UniProtKB:  Q16186
NIH Common Fund Data Resources
PHAROS:  Q16186 GTEx:  ENSG00000130706

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquilin-2	B	78	Homo sapiens	Mutation(s): 0  Gene Names: UBQLN2, N4BP4, PLIC2, HRIHFB2157
Find proteins for Q9UHD9 (Homo sapiens) Explore Q9UHD9  Go to UniProtKB:  Q9UHD9
NIH Common Fund Data Resources
PHAROS:  Q9UHD9 GTEx:  ENSG00000188021

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2NBV Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-12 
• Released Date: 2016-07-20 
Deposition Author(s): Chen, X., Walters, K.J.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Database references