6M2D

MUL1-RING domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

MUL1-RING recruits the substrate, p53-TAD as a complex with UBE2D2-UB conjugate.

Lee, M.S.Lee, S.O.Choi, J.Ryu, M.Lee, M.K.Kim, J.H.Hwang, E.Lee, C.K.Chi, S.W.Ryu, K.S.

(2022) FEBS J 

  • DOI: https://doi.org/10.1111/febs.16360
  • Primary Citation of Related Structures:  
    6M2C, 6M2D, 7BOL

  • PubMed Abstract: 

    The RING domain of MUL1 (RING MUL1 ) alone mediates ubiquitylation of the p53-transactivation domain (TAD p53 ). To elucidate the mechanism underlying the simultaneous recruitment of UBE2D2 and the substrate TAD p53 by RING MUL1 , we determined the complex structure of RING MUL1 :UBE2D2 and studied the interaction between RING MUL1 and TAD p53 in the presence of UBE2D2-UB thioester (UBE2D2~UB) mimetics. The RING MUL1 -binding induced the closed conformation of UBE2D2 S22R/C85S -UB K48R oxyester (UBE2D2 RS -UB R OE ), and strongly accelerated its hydrolysis, which was suppressed by the additional N77A-mutation of UBE2D2. Interestingly, UBE2D2 S22R/N77A/C85S -UB K48R oxyester (UBE2D2 RAS -UB R OE ) already formed a closed conformation in the absence of RING MUL1 . Although TAD p53 exhibited weak binding for RING MUL1 or UBE2D2 alone, its binding affinity was enhanced and even further for RING MUL1 :UBE2D2 and RING MUL1 :UBE2D2 RAS -UB R OE , respectively. The recognition of TAD p53 by RING MUL1 as a complex with UBE2D2~UB is related to the multivalency of the binding events and underlies the ability of RING MUL1 to ubiquitylate the intrinsically disordered protein, TAD p53 .


  • Organizational Affiliation

    Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial ubiquitin ligase activator of NFKB 1
A, B, C, D, E
57Homo sapiensMutation(s): 0 
Gene Names: MUL1C1orf166GIDEMAPLMULANRNF218
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q969V5 (Homo sapiens)
Explore Q969V5 
Go to UniProtKB:  Q969V5
GTEx:  ENSG00000090432 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969V5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
M [auth B]
N [auth B]
Q [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.226α = 90
b = 66.593β = 90
c = 68.271γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SO4Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Derived calculations
  • Version 1.2: 2022-04-20
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description