8C61

Structure of USP54 in complex with Lys63-linked diUbiquitin-PA

• PDB DOI: https://doi.org/10.2210/pdb8C61/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-01-11 Released: 2024-07-31 
• Deposition Author(s): Wendrich, K., Gersch, M.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.243 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Models: experimental, in silico

Literature

Structure of USP54 in complex with Lys63 linked diUbiquitin-PA

Wendrich, K., Gersch, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry, mass spectrometry

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: mass spectrometry, mass spectrometry

Macromolecule Content

• Total Structure Weight: 228.79 kDa 
• Atom Count: 14,892 
• Modelled Residue Count: 1,904 
• Deposited Residue Count: 2,004 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive ubiquitin carboxyl-terminal hydrolase 54	A, D, G, J	350	Homo sapiens	Mutation(s): 0  Gene Names: USP54, C10orf29
UniProt & NIH Common Fund Data Resources
Find proteins for Q70EL1 (Homo sapiens) Explore Q70EL1  Go to UniProtKB:  Q70EL1
PHAROS:  Q70EL1 GTEx:  ENSG00000166348

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, E, H, K	75	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, F, I, L	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	CA [auth J], DA [auth J], EA [auth J], M [auth A], N [auth A], O [auth A], T [auth D], U [auth D], V [auth D], X [auth G], Y [auth G], Z [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
AYE (Subject of Investigation/LOI)	AA [auth G], FA [auth J], P [auth A], W [auth D]	prop-2-en-1-amine C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N
CL	Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	BA [auth G], S [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.243 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.743	α = 90
b = 126.559	β = 90
c = 144.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
CRANK2	phasing
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Wendrich, K., Gersch, M.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	CGC-III-352S

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release