Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 8.86 kDa 
• Atom Count: 825 
• Modelled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

5NVG

Thr12 Phosphorylated Ubiquitin

• PDB DOI: 10.2210/pdb5NVG/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-04 Released: 2017-05-31 
• Deposition Author(s): Huguenin-Dezot, N.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.167 
• R-Value Work: 0.129 
• R-Value Observed: 0.131 

Literature

Biosynthesis and genetic encoding of phosphothreonine through parallel selection and deep sequencing.

Zhang, M.S., Brunner, S.F., Huguenin-Dezot, N., Liang, A.D., Schmied, W.H., Rogerson, D.T., Chin, J.W.

(2017) Nat Methods 14: 729-736

• PubMed: 28553966 
• DOI: 10.1038/nmeth.4302
• Primary Citation of Related Structures:  
  5NVG


• PubMed Abstract: 
  

The phosphorylation of threonine residues in proteins regulates diverse processes in eukaryotic cells, and thousands of threonine phosphorylations have been identified. An understanding of how threonine phosphorylation regulates biological function will be accelerated by general methods to biosynthesize defined phosphoproteins. Here we describe a rapid approach for directly discovering aminoacyl-tRNA synthetase-tRNA pairs that selectively incorporate non-natural amino acids into proteins; our method uses parallel positive selections combined with deep sequencing and statistical analysis and enables the direct, scalable discovery of aminoacyl-tRNA synthetase-tRNA pairs with mutually orthogonal substrate specificity. By combining a method to biosynthesize phosphothreonine in cells with this selection approach, we discover a phosphothreonyl-tRNA synthetase-tRNA _CUA pair and create an entirely biosynthetic route to incorporating phosphothreonine in proteins. We biosynthesize several phosphoproteins and demonstrate phosphoprotein structure determination and synthetic protein kinase activation.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, England, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	76	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.07 Å
• R-Value Free: 0.167 
• R-Value Work: 0.129 
• R-Value Observed: 0.131 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.46	α = 90
b = 24.74	β = 113.17
c = 47.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
iMOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-04 
• Released Date: 2017-05-31 
Deposition Author(s): Huguenin-Dezot, N.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_U105181009
Medical Research Council (United Kingdom)	United Kingdom	MC_UP_A024_1008

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2017-07-12
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence