6JLQ

Crystal structure of human USP46-WDR48-WDR20 complex

• PDB DOI: https://doi.org/10.2210/pdb6JLQ/pdb

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


• Deposited: 2019-03-06 Released: 2019-07-10 
• Deposition Author(s): Zhu, H., Zhang, T., Ding, J.
• Funding Organization(s): National Natural Science Foundation of China, Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.272 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 

Literature

Structural insights into the activation of USP46 by WDR48 and WDR20.

Zhu, H., Zhang, T., Wang, F., Yang, J., Ding, J.

(2019) Cell Discov 5: 34-34

• PubMed: 31632687 
• DOI: https://doi.org/10.1038/s41421-019-0102-1
• Primary Citation of Related Structures:  
  6JLQ

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031 China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 160.45 kDa 
• Atom Count: 9,327 
• Modelled Residue Count: 1,205 
• Deposited Residue Count: 1,416 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 46	A	352	Homo sapiens	Mutation(s): 0  Gene Names: USP46 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P62068 (Homo sapiens) Explore P62068  Go to UniProtKB:  P62068
PHAROS:  P62068 GTEx:  ENSG00000109189

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 48	B	620	Homo sapiens	Mutation(s): 0  Gene Names: WDR48
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
WD repeat-containing protein 20,highly similar to WD repeat protein 20,WD repeat-containing protein 20	C	444	Homo sapiens, Bos mutus	Mutation(s): 0  Gene Names: WDR20, M91_05678
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBZ3 (Homo sapiens) Explore Q8TBZ3  Go to UniProtKB:  Q8TBZ3
PHAROS:  Q8TBZ3 GTEx:  ENSG00000140153

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.272 
• R-Value Work: 0.247 
• R-Value Observed: 0.248 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.23	α = 90
b = 217.23	β = 90
c = 223.933	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Zhu, H., Zhang, T., Ding, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	--
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description