6JLQ | pdb_00006jlq

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.272 (Depositor), 0.275 (DCC)
R-Value Work:
0.247 (Depositor), 0.252 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-019-0102-1
Primary Citation Related Structures:
6JLQ

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62068
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TAF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TBZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A] G [auth B] H [auth B] I [auth B] J [auth B] 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		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.272 (Depositor), 0.275 (DCC)
R-Value Work: 0.247 (Depositor), 0.252 (DCC)
R-Value Observed: 0.248 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-10

Deposition Author(s):

Zhu, H.

Zhang, T.

Ding, J.

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

Revision History (Full details and data files)

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