5NVG

Thr12 Phosphorylated Ubiquitin

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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B A76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
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 = 50.46α = 90
b = 24.74β = 113.17
c = 47.65γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
PHASERphasing
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-04 
  • Released Date: 2017-05-31 
    • Deposition Author(s): Huguenin-Dezot, N.
Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105181009
Medical Research Council (United Kingdom)United KingdomMC_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