8J1R

cryo-EM structures of Ufd4 in complex with Ubc4-Ub

• PDB DOI: https://doi.org/10.2210/pdb8J1R/pdb
• EM Map EMD-35931: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae BY4741, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-13 Released: 2024-04-17 
• Deposition Author(s): Ai, H.S., Mao, J.X., Wu, X.W., Cai, H.Y., Pan, M., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Visualization of HECT-E3 Ufd4 accepting and transferring Ubiquitin to Form K29/K48-branched Polyubiquitination on N-degron. bioRxiv,doi: ttps://doi.org/10.1101/2023.05.23.542033

Mao, J.X., Ai, H.S., Wu, X.W., Cai, H.Y., Pan, M., Liu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 184.47 kDa 
• Atom Count: 6,497 
• Modelled Residue Count: 823 
• Deposited Residue Count: 1,631 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin fusion degradation protein 4	A	1,483	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: UFD4, YKL010C, YKL162 EC: 2.3.2 (PDB Primary Data), 2.3.2.26 (PDB Primary Data)
UniProt
Find proteins for P33202 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33202  Go to UniProtKB:  P33202

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 4	B [auth C]	148	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: UBC4, YBR082C, YBR0745 EC: 2.3.2.23
UniProt
Find proteins for P15731 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15731  Go to UniProtKB:  P15731

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Ai, H.S., Mao, J.X., Wu, X.W., Cai, H.Y., Pan, M., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22137005, 92253302, 22227810, 22277073, 92253302,

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release