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NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
15N T1
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
2
15N T2
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
3
HETERONUCLEAR NOE
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
4
HSQC
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
5
TOCSY
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
6
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
7
DI-UBIQUITIN, 90% WATER/10% D20
20mM
6.8
AMBIENT
298.0
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
THE STRUCTURE WAS DETERMINED WITH PROGRAM ELM USING COMPLETE ROTATIONAL DIFFUSION TENSOR OF DI-UBIQUITIN AS EXPERIMENTAL RESTRAINT FOR BOTH ORIENTATION AND POSITIONING OF THE INDIVIDUAL UBIQUITIN DOMAINS WITHIN THE
MOLECULE. UBIQUITIN DOMAINS WHERE ORIENTED BY A RIGID BODY
ROTATION USING EXPERIMENTALLY DERIVED PRINCIPAL AXES FRAME OF
THE DIFFUSION TENSOR (SEE REFERENCE 2). THE RELATIVE DOMAIN
POSITIONS IN DI-UBIQUITIN WERE DETERMINED BY A RIGID BODY
TRANSLATION USING ALL COMPONENTS OF THE EXPERIMENTALLY DERIVED
ROTATIONAL DIFFUSION TENSOR AS RESTRAINTS.
FOR EACH UBIQUITIN DOMAIN THE STRUCTURE OF THE FIRST CONFORMER
OF PDB ENTRY 1D3Z WAS ASSUMED. THE DEPOSITED CONFORMATION
REPRESENTS ONE OF THE TWO EXPERIMENTALLY DETECTABLE
CONFORMATIONS OF DI-UBIQUITIN AT PH 6.8. THE OCCUPATION
PROBABILITY OF THIS CONFORMATION IS APPROXIMATELY 90%. CHAIN A
CORRESPONDS TO UBIQUITIN DOMAIN THAT HAS A FREE C-TERMINUS IN
DI-UBIQUITIN. CHAIN B CORRESPONDS TO UBIQUITIN DOMAIN THAT IN
DI-UBIQUITIN IS LINKED VIA AN ISOPEPTIDE BOND BETWEEN ITS C-
TERMINAL GLY76 AND LYS48 OF CHAIN A. THE ISOPEPTIDE BOND WAS
PRESENT IN THE DI-UBIQUITIN MOLECULE IN THIS STUDY. HOWEVER,
BECAUSE THIS STRUCTURE WAS OBTAINED BY A RIGID BODY ROTATION
AND TRANSLATION AND NO CONSTRAINTS REPRESENTING
THE INTERDOMAIN LINKAGE WERE INCLUDED, THE ISOPEPTIDE LINKAGE
IS NOT PRESENT IN THE STRUCTURE. FLEXIBLE C-TERMINI OF BOTH
UBIQUTIN DOMAINS (RESIDUES 73-76)WERE EXCLUDED FROM THE NMR
RATA ANALYSIS AND THEREFORE ARE NOT PRESENT IN THIS STRUCTURE.