9DI2 | pdb_00009di2

Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex

• PDB DOI: https://doi.org/10.2210/pdb9DI2/pdb
• EM Map EMD-46896: EMDB EMDataResource

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


• Deposited: 2024-09-04 Released: 2025-09-17 
• Deposition Author(s): Griffith, J.P.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the USP1-UAF1-Ubiquitin-VS complex

Wylie, A.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 173.36 kDa 
• Atom Count: 8,097 
• Modeled Residue Count: 1,017 
• Deposited Residue Count: 1,537 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 48	A	677	Homo sapiens	Mutation(s): 0  Gene Names: WDR48, KIAA1449, UAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAF3 (Homo sapiens) Explore Q8TAF3  Go to UniProtKB:  Q8TAF3
PHAROS:  Q8TAF3 GTEx:  ENSG00000114742

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 1	B	785	Homo sapiens	Mutation(s): 0  Gene Names: USP1 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94782 (Homo sapiens) Explore O94782  Go to UniProtKB:  O94782
PHAROS:  O94782 GTEx:  ENSG00000162607

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C	75	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 GTEx:  ENSG00000150991

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A4Y	E [auth B]	3-(methanesulfonyl)propan-1-amine C4 H11 N O2 S QUYFSHOLLKVPGX-UHFFFAOYSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Griffith, J.P.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release