9YC2 | pdb_00009yc2

Crystal structure of USP49 ZnF-UBP domain

• PDB DOI: https://doi.org/10.2210/pdb9YC2/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2025-09-18 Released: 2025-10-29 
• Deposition Author(s): Alexandrovics, J.A., Komander, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

The ZnF-UBP domain regulates USP16 activity by dislodging ubiquitin from the active site

Alexandrovics, J.A., Agrata, R., Schenk, P., Cerra, A., Nachbur, U., Babon, J.J., Komander, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 12.55 kDa 
• Atom Count: 1,059 
• Modeled Residue Count: 105 
• Deposited Residue Count: 105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 49	A	105	Homo sapiens	Mutation(s): 0  Gene Names: USP49 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q70CQ1 (Homo sapiens) Explore Q70CQ1  Go to UniProtKB:  Q70CQ1
PHAROS:  Q70CQ1 GTEx:  ENSG00000164663

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.739	α = 90
b = 47.22	β = 90
c = 55.247	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Alexandrovics, J.A., Komander, D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1178122

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release