9HNW

USP1-UAF1 bound to Lys63-linked diubiquitin

• PDB DOI: https://doi.org/10.2210/pdb9HNW/pdb
• EM Map EMD-52316: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-12-11 Released: 2025-02-12 
• Deposition Author(s): Keijzer, N., Sakoltchik, J., Sixma, T.K.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), Health-Holland

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

USP1-UAF1 bound to Lys63-linked diubiquitin

Keijzer, N., Sixma, T.K., Sakoltchik, J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 189.13 kDa 
• Atom Count: 9,349 
• Modelled Residue Count: 1,179 
• Deposited Residue Count: 1,677 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 1	A	813	Homo sapiens	Mutation(s): 2  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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 48	B	712	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	C	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	D	76	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB	D	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Keijzer, N., Sakoltchik, J., Sixma, T.K.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	TOP714.016.002
Health-Holland	Netherlands	LSHM21048-H045

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release