8J1P

Cryo-EM structure of Ufd4 in complex with K29/48 triUb

• PDB DOI: https://doi.org/10.2210/pdb8J1P/pdb
• EM Map EMD-35929: EMDB EMDataResource

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae, Homo sapiens
• 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., 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: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Insights into the Molecular Mechanism of Ufd4-catalyzed Elongation of K48-linked Ubiquitin Chain through Lys29 Linkage

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 193.73 kDa 
• Atom Count: 11,523 
• Modelled Residue Count: 1,458 
• Deposited Residue Count: 1,711 
• Unique protein chains: 3

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	B [auth C], D [auth E]	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 GTEx:  ENSG00000170315

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C [auth D]	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.31 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., Pan, M., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

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