8TTQ | pdb_00008ttq

Cryo-EM structure of the inner MKLN1 dimer from an autoinhibited MKLN1 tetramer

• PDB DOI: https://doi.org/10.2210/pdb8TTQ/pdb
• EM Map EMD-41612: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2023-08-14 Released: 2024-09-11 
• Deposition Author(s): Chana, C.K., Keszei, A.F.A., Sicheri, F.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

FAM72A degrades UNG2 through the GID/CTLH complex to promote mutagenic repair during antibody maturation.

Barbulescu, P., Chana, C.K., Wong, M.K., Ben Makhlouf, I., Bruce, J.P., Feng, Y., Keszei, A.F.A., Wong, C., Mohamad-Ramshan, R., McGary, L.C., Kashem, M.A., Ceccarelli, D.F., Orlicky, S., Fang, Y., Kuang, H., Mazhab-Jafari, M., Pezo, R.C., Bhagwat, A.S., Pugh, T.J., Gingras, A.C., Sicheri, F., Martin, A.

(2024) Nat Commun 15: 7541-7541

• PubMed: 39215025 
• DOI: https://doi.org/10.1038/s41467-024-52009-x
• Primary Citation of Related Structures:  
  8TTQ


• PubMed Abstract: 
  

  A diverse antibody repertoire is essential for humoral immunity. Antibody diversification requires the introduction of deoxyuridine (dU) mutations within immunoglobulin genes to initiate somatic hypermutation (SHM) and class switch recombination (CSR). dUs are normally recognized and excised by the base excision repair (BER) protein uracil-DNA glycosylase 2 (UNG2). However, FAM72A downregulates UNG2 permitting dUs to persist and trigger SHM and CSR. How FAM72A promotes UNG2 degradation is unknown. Here, we show that FAM72A recruits a C-terminal to LisH (CTLH) E3 ligase complex to target UNG2 for proteasomal degradation. Deficiency in CTLH complex components result in elevated UNG2 and reduced SHM and CSR. Cryo-EM structural analysis reveals FAM72A directly binds to MKLN1 within the CTLH complex to recruit and ubiquitinate UNG2. Our study further suggests that FAM72A hijacks the CTLH complex to promote mutagenesis in cancer. These findings show that FAM72A is an E3 ligase substrate adaptor critical for humoral immunity and cancer development.

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Organizational Affiliation: 
• Department of Immunology, University of Toronto, Toronto, ON, Canada.
Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada.
Department of Chemistry, Wayne State University, Detroit, MI, USA.
Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA.
Sunnybrook Health Sciences Center, Toronto, ON, Canada.
Department of Biochemistry, University of Toronto, Toronto, ON, Canada. [e-mail].
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada. [e-mail].
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. [e-mail].
Department of Immunology, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 174.4 kDa 
• Atom Count: 9,279 
• Modeled Residue Count: 1,212 
• Deposited Residue Count: 1,510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Muskelin	A, B	755	Homo sapiens	Mutation(s): 0  Gene Names: MKLN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL63 (Homo sapiens) Explore Q9UL63  Go to UniProtKB:  Q9UL63
PHAROS:  Q9UL63 GTEx:  ENSG00000128585

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.27 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Chana, C.K., Keszei, A.F.A., Sicheri, F.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-178026
Canadian Institutes of Health Research (CIHR)	Canada	PJT-180338
Canadian Institutes of Health Research (CIHR)	Canada	PJT-186218

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release