6PGV | pdb_00006pgv

Human Josephin-2 in complex with ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb6PGV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-24 Released: 2019-10-23 
• Deposition Author(s): Grasty, K.C., Weeks, S.D., Loll, P.J.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.224 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 

Literature

Structural insights into the activity and regulation of human Josephin-2

Grasty, K.C., Weeks, S.D., Loll, P.J.

(2019) J Struct Biol 3: 100011

• DOI: https://doi.org/10.1016/j.yjsbx.2019.100011

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.44 kDa 
• Atom Count: 1,825 
• Modeled Residue Count: 227 
• Deposited Residue Count: 263 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Josephin-2	A	188	Homo sapiens	Mutation(s): 0  Gene Names: JOSD2, SBBI54 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAC2 (Homo sapiens) Explore Q8TAC2  Go to UniProtKB:  Q8TAC2
PHAROS:  Q8TAC2 GTEx:  ENSG00000161677

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NEH	C [auth B]	ETHANAMINE C2 H7 N QUSNBJAOOMFDIB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.224 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.12	α = 90
b = 102.12	β = 90
c = 92.2	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Grasty, K.C., Weeks, S.D., Loll, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS065140

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary