Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 12.57 kDa 
• Atom Count: 726 
• Residue Count: 93 
• Unique protein chains: 2

6NJG

Ubiquitin Variant in Complex with Ubiquitin Interacting Motif

• DOI: 10.2210/pdb6NJG/pdb
• Entry: 6NJG supersedes: 5UCL

• Classification: PROTEIN BINDING
• Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-01-03 Released: 2019-03-06 
• Deposition Author(s): Manczyk, N., Sicheri, F.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.244 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif.

Manczyk, N., Veggiani, G., Gish, G.D., Yates, B.P., Ernst, A., Sidhu, S.S., Sicheri, F.

(2019) Protein Sci 28: 848-856

• PubMed: 30793400 
• DOI: 10.1002/pro.3593
• Primary Citation of Related Structures:  
  6NJG


• PubMed Abstract: 
  

We previously described structural and functional characterization of the first ubiquitin variant (UbV), UbV.v27.1, engineered by phage display to bind with high affinity to a specific ubiquitin interacting motif (UIM). We identified two substitutions relative to ubiquitin (Gly10Val/His68Tyr) that were critical for enhancing binding affinity but could only rationalize the mechanism of action of the Tyr68 substitution. Here, we extend our characterization and uncover the mechanism by which the Val10 substitution enhances binding affinity. We show that Val10 in UbV.v27.1 drives UbV dimerization through an intermolecular β-strand exchange. Dimerization serves to increase the contact surface between the UIM and UbV and also affords direct contacts between two UIMs through an overall 2:2 binding stoichiometry. Our identification of the role of Val10 in UbV dimerization suggests a general means for the development of dimeric UbVs with improved affinity and specificity relative to their monomeric UbV counterparts. Statement: Previously, we used phage display to engineer a UbV that bound tightly and specifically to a UIM. Here, we discovered that tight binding is partly due to the dimerization of the UbV, which increases the contact surface between the UbV and UIM. We show that UbV dimerization is dependent on the Gly10Val substitution, and posit that dimerization may provide a general means for engineering UbVs with improved binding properties.

---

Organizational Affiliation: 

Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 27	B	24	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: VPS27, DID7, GRD11, SSV17, VPL23, VPT27, YNR006W, N2038
Find proteins for P40343 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40343  Go to UniProtKB:  P40343

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	C	89	Homo sapiens	Mutation(s): 18  Gene Names: UBB
Find proteins for J3QS39 (Homo sapiens) Explore J3QS39  Go to UniProtKB:  J3QS39

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.244 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.613	α = 90
b = 44.613	β = 90
c = 104.343	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-03 
• Released Date: 2019-03-06 
Deposition Author(s): Manczyk, N., Sicheri, F.
• This entry supersedes: 5UCL

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	FDN-143277

Revision History 

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence