Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 71.89 kDa 
• Atom Count: 4978 
• Modelled Residue Count: 628 
• Deposited Residue Count: 630 
• Unique protein chains: 4

6N13

UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin

• DOI: 10.2210/pdb6N13/pdb
• BMRB: 27664

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-11-08 Released: 2018-11-28 
• Deposition Author(s): Condos, T.E.C., Dunkerley, K.M., Freeman, E.A., Barber, K.R., Aguirre, J.D., Chaugule, V.K., Xiao, Y., Konermann, L., Walden, H., Shaw, G.S.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.

Condos, T.E., Dunkerley, K.M., Freeman, E.A., Barber, K.R., Aguirre, J.D., Chaugule, V.K., Xiao, Y., Konermann, L., Walden, H., Shaw, G.S.

(2018) EMBO J 37

• PubMed: 30446597 
• DOI: 10.15252/embj.2018100014
• Primary Citation of Related Structures:  
  6N13


• PubMed Abstract: 
  

The E3 ligase parkin ubiquitinates outer mitochondrial membrane proteins during oxidative stress and is linked to early-onset Parkinson's disease. Parkin is autoinhibited but is activated by the kinase PINK1 that phosphorylates ubiquitin leading to parkin recruitment, and stimulates phosphorylation of parkin's N-terminal ubiquitin-like (pUbl) domain. How these events alter the structure of parkin to allow recruitment of an E2~Ub conjugate and enhanced ubiquitination is an unresolved question. We present a model of an E2~Ub conjugate bound to the phospho-ubiquitin-loaded C-terminus of parkin, derived from NMR chemical shift perturbation experiments. We show the UbcH7~Ub conjugate binds in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR and mass spectrometry experiments indicate the RING0/RING2 interface is re-modelled, remote from the E2 binding site, and this alters the reactivity of the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer. Our experiments provide evidence that parkin phosphorylation and E2~Ub recruitment act synergistically to enhance a weak interaction of the pUbl domain with the RING0 domain and rearrange the location of the RING2(Rcat) domain to drive parkin activity.

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Related Citations: 

• Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity.
  Kumar, A., Chaugule, V.K., Condos, T.E.C., Barber, K.R., Johnson, C., Toth, R., Sundaramoorthy, R., Knebel, A., Shaw, G.S., Walden, H.
  (2017) Nat Struct Mol Biol 24: 475

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Organizational Affiliation: 

Department of Biochemistry, The University of Western Ontario, London, ON, Canada [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase parkin	A [auth B]	322	Homo sapiens	Mutation(s): 1  Gene Names: PRKN, PARK2 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	B [auth D]	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 L3	C	156	Homo sapiens	Mutation(s): 3  Gene Names: UBE2L3, UBCE7, UBCH7 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P68036 (Homo sapiens) Explore P68036  Go to UniProtKB:  P68036
PHAROS:  P68036 GTEx:  ENSG00000185651

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoubiquitin	D [auth A]	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	D [auth A]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 6N13 Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-08 
• Released Date: 2018-11-28 
Deposition Author(s): Condos, T.E.C., Dunkerley, K.M., Freeman, E.A., Barber, K.R., Aguirre, J.D., Chaugule, V.K., Xiao, Y., Konermann, L., Walden, H., Shaw, G.S.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-14606

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Database references
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence, Data collection, Database references