Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 52230.24 
• Atom Count: 3642 
• Residue Count: 452 
• Unique protein chains: 3

5O44

Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages.

• DOI: 10.2210/pdb5O44/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Musca domestica, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2017-05-26 Released: 2017-11-08 
• Deposition Author(s): Padala, P., Isupov, M.N., Wiener, R.
• Funding Organization(s): null 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 

Literature

The Crystal Structure and Conformations of an Unbranched Mixed Tri-Ubiquitin Chain Containing K48 and K63 Linkages.

Padala, P., Soudah, N., Giladi, M., Haitin, Y., Isupov, M.N., Wiener, R.

(2017) J. Mol. Biol. 429: 3801-3813

• PubMed: 29111344 
• DOI: 10.1016/j.jmb.2017.10.027


• PubMed Abstract: 
  

The ability of ubiquitin to function in a wide range of cellular processes is ascribed to its capacity to cause a diverse spectrum of modifications. While a target protein can be modified with monoubiquitin, it can also be modified with ubiquitin chains. The latter include seven types of homotypic chains as well as mixed ubiquitin chains. In a mixed chain, not all the isopeptide bonds are restricted to a specific lysine of ubiquitin, resulting in a chain possessing more than one type of linkage. While structural characterization of homotypic chains has been well elucidated, less is known about mixed chains. Here we present the crystal structure of a mixed tri-ubiquitin chain at 3.1-Å resolution. In the structure, the proximal ubiquitin is connected to the middle ubiquitin via K48 and these two ubiquitins adopt a compact structure as observed in K48 di-ubiquitin. The middle ubiquitin links to the distal ubiquitin via its K63 and these ubiquitins adopt two conformations, suggesting a flexible structure. Using small-angle X-ray scattering, we unexpectedly found differences between the conformational ensembles of the above tri-ubiquitin chains and chains possessing the same linkages but in the reverse order. In addition, cleavage of the K48 linkage by DUB is faster if this linkage is at the distal end. Taken together, our results suggest that in mixed chains, not only the type of the linkages but also their sequence determine the structural and functional properties of the chain.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	A, E	76	Musca domestica	Mutation(s): 1
Find proteins for Q45TR8 (Musca domestica) Go to UniProtKB:  Q45TR8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	C, B	74	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	D, F	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, E	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	A, D, E	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 110.767	α = 90.00
b = 110.767	β = 90.00
c = 417.004	γ = 120.00

Software Package:

Software Name	Purpose
Aimless	data scaling
XDS	data reduction
REFMAC	refinement
MOLREP	phasing
xia2	data reduction
DM	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-26 
• Released Date: 2017-11-08 
• Deposition Author(s): Padala, P., Isupov, M.N., Wiener, R.

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Funding Organization	Location	Grant Number
	Israel	--

Revision History 

• Version 1.0: 2017-11-08
  Type: Initial release
• Version 1.1: 2017-11-15
  Type: Database references
• Version 1.2: 2017-12-06
  Type: Database references
• Version 1.3: 2019-05-08
  Type: Advisory, Data collection, Derived calculations