5KHY

Crystal structure of oxime-linked K6 diubiquitin

PDB DOI: https://doi.org/10.2210/pdb5KHY/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Bacteria
Mutation(s): No

Deposited: 2016-06-16 Released: 2016-09-14
Deposition Author(s): Stanley, M., Virdee, S.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.331
R-Value Work: 0.282
R-Value Observed: 0.295

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Genetically Directed Production of Recombinant, Isosteric and Nonhydrolysable Ubiquitin Conjugates.

Stanley, M., Virdee, S.

(2016) Chembiochem 17: 1472-1480

PubMed: 27197715 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cbic.201600138
Primary Citation of Related Structures:
5KHY

PubMed Abstract:
We describe the genetically directed incorporation of aminooxy functionality into recombinant proteins by using a mutant Methanosarcina barkeri pyrrolysyl-tRNA synthetase/tRNACUA pair. This allows the general production of nonhydrolysable ubiquitin conjugates of recombinant origin by bioorthogonal oxime ligation. This was exemplified by the preparation of nonhydrolysable versions of diubiquitin, polymeric ubiquitin chains and ubiquitylated SUMO. The conjugates exhibited unrivalled isostery with the native isopeptide bond, as inferred from structural and biophysical characterisation. Furthermore, the conjugates functioned as nanomolar inhibitors of deubiquitylating enzymes and were recognised by linkage-specific antibodies. This technology should provide a versatile platform for the development of powerful tools for studying deubiquitylating enzymes and for elucidating the cellular roles of diverse polyubiquitin linkages.

Organizational Affiliation

MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK.

Macromolecule Content

Total Structure Weight: 17.54 kDa
Atom Count: 1,096
Modelled Residue Count: 148
Deposited Residue Count: 148
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	73	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 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	75	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 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
ETA Query on ETA Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	ETHANOLAMINE C₂ H₇ N O HZAXFHJVJLSVMW-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.331
R-Value Work: 0.282
R-Value Observed: 0.295
Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.975	α = 90
b = 103.975	β = 90
c = 103.975	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Stanley, M.

Virdee, S.

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_UU_12016/8

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2017-09-13
Changes: Advisory, Author supporting evidence
Version 1.2: 2018-11-21
Changes: Advisory, Data collection, Derived calculations
Version 1.3: 2019-10-16
Changes: Data collection
Version 2.0: 2023-11-15
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations