2YH1
Model of human U2AF65 tandem RRM1 and RRM2 domains with eight-site uridine binding
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 600 |
3 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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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 | |
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Conformer Selection Criteria | LOWEST ENERGY |
Conformers Calculated Total Number | 125 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (n/a) |
Additional NMR Experimental Information | |
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Details | THE STRUCTURE WAS DETERMINED USING A MULTI-STEP PROTOCOL AS DESCRIBED IN REMARK 3. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | CNS | 1.2 | BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, READ,RICE,SIMONSON,WARREN |
2 | structure solution | Sparky |