5YMY

The structure of the complex between Rpn13 and K48-diUb


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/s41421-019-0089-7

  • 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 <sup>NTD </sup>) and Ub monomer h ...

    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.


    Organizational Affiliation

    3University of Chinese Academy of Sciences, Beijing, 100049 China.,5Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei Province 430074 China.,1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,2National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China.,4Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310027 China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B
76Homo sapiensMutation(s): 1 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasomal ubiquitin receptor ADRM1
C
150Homo sapiensMutation(s): 0 
Gene Names: ADRM1 (GP110)
Find proteins for Q16186 (Homo sapiens)
Go to Gene View: ADRM1
Go to UniProtKB:  Q16186
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0501200
National Basic Research Program of China(973 Program)China2013CB910200
National Natural Science Foundation of ChinaChina31770799
National Natural Science Foundation of ChinaChina81573400
National Natural Science Foundation of ChinaChina31500595
National Natural Science Foundation of ChinaChina31400735
National Natural Science Foundation of ChinaChina31400644

Revision History 

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