Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.92 kDa 
• Atom Count: 2144 
• Modelled Residue Count: 266 
• Deposited Residue Count: 302 
• Unique protein chains: 3

5YMY

The structure of the complex between Rpn13 and K48-diUb

• PDB DOI: 10.2210/pdb5YMY/pdb

• Classification: PROTEIN BINDING/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-22 Released: 2019-03-13 
• Deposition Author(s): Liu, Z., Dong, X., Gong, Z., Yi, H.W., Liu, K., Yang, J., Zhang, W.P., Tang, C.
• Funding Organization(s): Ministry of Science and Technology (China), National Basic Research Program of China(973 Program), National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 240 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13.

Liu, Z., Dong, X., Yi, H.W., Yang, J., Gong, Z., Wang, Y., Liu, K., Zhang, W.P., Tang, C.

(2019) Cell Discov 5: 19-19

• PubMed: 30962947 
• DOI: 10.1038/s41421-019-0089-7
• Primary Citation of Related Structures:  
  5YMY


• PubMed Abstract: 
  

The interaction between K48-linked ubiquitin (Ub) chain and Rpn13 is important for proteasomal degradation of ubiquitinated substrate proteins. Only the complex structure between the N-terminal domain of Rpn13 (Rpn13 ^NTD ) and Ub monomer has been characterized, while it remains unclear how Rpn13 specifically recognizes K48-linked Ub chain. Using single-molecule FRET, here we show that K48-linked diubiquitin (K48-diUb) fluctuates among distinct conformational states, and a preexisting compact state is selectively enriched by Rpn13 ^NTD . The same binding mode is observed for full-length Rpn13 and longer K48-linked Ub chain. Using solution NMR spectroscopy, we have determined the complex structure between Rpn13 ^NTD and K48-diUb. In this structure, Rpn13 ^NTD simultaneously interacts with proximal and distal Ub subunits of K48-diUb that remain associated in the complex, thus corroborating smFRET findings. The proximal Ub interacts with Rpn13 ^NTD similarly as the Ub monomer in the known Rpn13 ^NTD :Ub structure, while the distal Ub binds to a largely electrostatic surface of Rpn13 ^NTD . Thus, a charge-reversal mutation in Rpn13 ^NTD weakens the interaction between Rpn13 and K48-linked Ub chain, causing accumulation of ubiquitinated proteins. Moreover, physical blockage of the access of the distal Ub to Rpn13 ^NTD with a proximity-attached Ub monomer can disrupt the interaction between Rpn13 and K48-diUb. Taken together, the bivalent interaction of K48-linked Ub chain with Rpn13 provides the structural basis for Rpn13 linkage selectivity, which opens a new window for modulating proteasomal function.

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Organizational Affiliation: 

5Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei Province 430074 China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasomal ubiquitin receptor ADRM1	C	150	Homo sapiens	Mutation(s): 0  Gene Names: ADRM1, GP110
UniProt & NIH Common Fund Data Resources
Find proteins for Q16186 (Homo sapiens) Explore Q16186  Go to UniProtKB:  Q16186
PHAROS:  Q16186 GTEx:  ENSG00000130706

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 240 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 5YMY Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-10-22 
• Released Date: 2019-03-13 
Deposition Author(s): Liu, Z., Dong, X., Gong, Z., Yi, H.W., Liu, K., Yang, J., Zhang, W.P., Tang, C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0501200
National Basic Research Program of China(973 Program)	China	2013CB910200
National Natural Science Foundation of China	China	31770799
National Natural Science Foundation of China	China	81573400
National Natural Science Foundation of China	China	31500595
National Natural Science Foundation of China	China	31400735
National Natural Science Foundation of China	China	31400644

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Database references