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Model of human U2AF65 tandem RRM1 and RRM2 domains with eight-site uridine binding
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
1H
90% WATER/10% D2O
70 mM
6.5
1.0 atm
295.0
2
15N HSQC (PRE)
90% WATER/10% D2O
70 mM
6.5
1.0 atm
295.0
3
1H
90% WATER/10% D2O
70 mM
6.5
1.0 atm
295.0
4
15N TROSY (HN-N RDC)
90% WATER/10% D2O
70 mM
6.5
1.0 atm
295.0
5
3D HNCO (N-CO RDC)
90% WATER/10% D2O
70 mM
6.5
1.0 atm
295.0
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
600
2
Bruker
AVANCE
600
3
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
MODIFIED ARIA
STRUCTURE CALCULATION INCLUDED DISTANCE RESTRAINTS BASED ON PARAMAGNETIC RELAXATION ENHANCEMENT DATA FROM TEN INDEPENDENT CYSTEINE MUTANTS (N155C, A164C, A171C, L187C, A188C, T209C, D273C, S281C, A287C AND A318C) COVALENTLY MODIFIED BY 3-(2-IODOACETAMIDO)-2,2,5,5, TETRAMETHYL-1-PYRROLIDINYLOXY RADICAL (IODOACETAMIDO- PROXYL). THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL. FIRST WITH REFINEMENT OF INDIVIDUAL STRUCTURED DOMAINS FOR RRM1 AND RRM2 OF U2AF65. THE INITIAL COORDINATES OF THE ISOLATED DOMAINS WERE BASED ON PDB ENTRY 2G4B BY SICKMIER ET AL. 2006 (SEE REMARK 1 REFERENCE). SECOND STEP WAS ADDITION AND RANDOMIZATION OF FLEXIBLE AND LINKER RESIDUES. THE THIRD STEP WAS MODEL CALCULATION USING RDC ORIENTATION, PRE-BASED DISTANCE, TALOS DIHEDRAL AND HYDROGEN BOND RESTRAINTS WITH THE RRM1 AND RRM2 DOMAINS RESTRAINED TO THEIR INITIAL STARTING STRUCTURES. INTER- MOLECULAR PROTEIN-RNA DISTANCE RESTRAINTS WERE BASED ON ATOMIC DETAILS FROM PDB ENTRY 2G4B AND ASSUMED AN EIGHT- URIDINE BINDING MODE FOR U2AF65 RRM1-RRM2.
CNS
NMR Ensemble Information
Conformer Selection Criteria
LOWEST ENERGY
Conformers Calculated Total Number
125
Conformers Submitted Total Number
10
Representative Model
1 (n/a)
Additional NMR Experimental Information
Details
THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL AS DESCRIBED IN REMARK 3.