Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 67.00 kDa 
• Atom Count: 4832 
• Modelled Residue Count: 555 
• Deposited Residue Count: 588 
• Unique protein chains: 4

4LDT

The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub

• DOI: 10.2210/pdb4LDT/pdb

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


• Deposited: 2013-06-25 Released: 2013-08-14 
• Deposition Author(s): Wiener, R., DiBello, A.T., Lombardi, P.M., Guzzo, C.M., Zhang, X., Matunis, M.J., Wolberger, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1.

Wiener, R., Dibello, A.T., Lombardi, P.M., Guzzo, C.M., Zhang, X., Matunis, M.J., Wolberger, C.

(2013) Nat Struct Mol Biol 20: 1033-1039

• PubMed: 23955022 
• DOI: 10.1038/nsmb.2655
• Primary Citation of Related Structures:  
  4LDT


• PubMed Abstract: 
  

OTUB1 is a Lys48-specific deubiquitinating enzyme that forms a complex in vivo with E2 ubiquitin (Ub)-conjugating enzymes including UBC13 and UBCH5. OTUB1 binds E2~Ub thioester intermediates and prevents ubiquitin transfer, thereby noncatalytically inhibiting accumulation of polyubiquitin. We report here that a second role of OTUB1-E2 interactions is to stimulate OTUB1 cleavage of Lys48 polyubiquitin. This stimulation is regulated by the ratio of charged to uncharged E2 and by the concentration of Lys48-linked polyubiquitin and free ubiquitin. Structural and biochemical studies of human and worm OTUB1 and UBCH5B show that the E2 enzyme stimulates binding of the Lys48 polyubiquitin substrate by stabilizing folding of the OTUB1 N-terminal ubiquitin-binding helix. Our results suggest that OTUB1-E2 complexes in the cell are poised to regulate polyubiquitin chain elongation or degradation in response to changing levels of E2 charging and available free ubiquitin.

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Organizational Affiliation: 

1] Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. [2] Howard Hughes Medical Institute, Baltimore, Maryland, USA. [3] [4].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin thioesterase otubain-like	A	288	Homo sapiens, Caenorhabditis elegans This entity is chimeric	Mutation(s): 0  Gene Names: OTUB1, OTB1, OTU1, HSPC263, C25D7.8, otub-1 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FW1 (Homo sapiens) Explore Q96FW1  Go to UniProtKB:  Q96FW1
PHAROS:  Q96FW1 GTEx:  ENSG00000167770
Find proteins for Q9XVR6 (Caenorhabditis elegans) Explore Q9XVR6  Go to UniProtKB:  Q9XVR6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin aldehyde	B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	C	148	Homo sapiens	Mutation(s): 1  Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	D	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], F [auth A], G [auth A], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
GLZ	B	L-PEPTIDE LINKING	C2 H5 N O		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.894	α = 90
b = 131.612	β = 90
c = 46.501	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-25 
• Released Date: 2013-08-14 
Deposition Author(s): Wiener, R., DiBello, A.T., Lombardi, P.M., Guzzo, C.M., Zhang, X., Matunis, M.J., Wolberger, C.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2013-09-25
  Changes: Database references
• Version 1.3: 2017-07-26
  Changes: Refinement description, Source and taxonomy