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

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

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, KIAA1449, UAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAF3 (Homo sapiens) Explore Q8TAF3  Go to UniProtKB:  Q8TAF3
PHAROS:  Q8TAF3

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

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