8IK6

pUbl depleted Parkin complex with pUbiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.234 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Additional feedforward mechanism of Parkin activation via binding of phospho-UBL and RING0 in trans.

Lenka, D.R.Dahe, S.V.Antico, O.Sahoo, P.Prescott, A.R.Muqit, M.M.K.Kumar, A.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.96699
  • Primary Citation of Related Structures:  
    8IK6, 8IKM, 8IKT, 8IKV, 8JWV

  • PubMed Abstract: 

    Loss-of-function Parkin mutations lead to early-onset of Parkinson's disease. Parkin is an auto-inhibited ubiquitin E3 ligase activated by dual phosphorylation of its ubiquitin-like (Ubl) domain and ubiquitin by the PINK1 kinase. Herein, we demonstrate a competitive binding of the phospho-Ubl and RING2 domains towards the RING0 domain, which regulates Parkin activity. We show that phosphorylated Parkin can complex with native Parkin, leading to the activation of autoinhibited native Parkin in trans . Furthermore, we show that the activator element (ACT) of Parkin is required to maintain the enzyme kinetics, and the removal of ACT slows the enzyme catalysis. We also demonstrate that ACT can activate Parkin in trans but less efficiently than when present in the cis molecule. Furthermore, the crystal structure reveals a donor ubiquitin binding pocket in the linker connecting REP and RING2, which plays a crucial role in Parkin activity.


  • Organizational Affiliation

    Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA [auth C],
C [auth A]
327Homo sapiensMutation(s): 8 
Gene Names: PRKNPARK2
EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O60260 (Homo sapiens)
Explore O60260 
Go to UniProtKB:  O60260
PHAROS:  O60260
GTEx:  ENSG00000185345 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60260
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinB [auth D],
D [auth B]
75Homo sapiensMutation(s): 0 
Gene Names: UBA52UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62987
Sequence Annotations
Expand
  • 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 
AA [auth A]
M [auth C]
N [auth C]
O [auth C]
P [auth C]
AA [auth A],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
Z [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth C]
F [auth C]
G [auth C]
H [auth C]
I [auth C]
E [auth C],
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B [auth D],
D [auth B]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.234 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.805α = 90
b = 187.805β = 90
c = 141.857γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaInnovative Young Biotechnology Award (DBT/12/IYBAl2019/03) and Ramalingaswami Fellowship (DBT/RLF/Re-entry/42/2019)

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Structure summary