BMRB: 25652Chemical shifts for the construct when bound to a stemloop RNA.
BMRB: 34766NMR solution structure of the N-terminal RRM and flanking linker regions of Polypyrimidine tract binding protein 1 using the CYANA CONSENSUS method.
Polypyrimidinetract-bindingprotein1 / PTB / 57 kDa RNA-binding protein PPTB-1 / Heterogeneous nuclear ribonucleoprotein I / hnRNP I
Mass: 13375.167 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTBP1, PTB / Plasmid: pTYB11 Details (production host): gene for construct inserted between the NdeI and Xho1 sites Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon-plus RIL / References: UniProt: P26599
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
2
isotropic
1
3D 1H-15N NOESY
1
2
2
isotropic
1
3D 1H-13C NOESY
2
3
1
isotropic
3
15N T1-relaxation-15HSQC
2
4
1
isotropic
3
15N T2-relaxation-T1rho-15NHSQC
2
5
1
isotropic
3
{1H}15N-NOE-15NHSQC
1
6
1
isotropic
2
relaxation-compensated IzNz Rex HSQC
1
7
1
isotropic
2
15N T2-relaxation-dispersion CPMG-15NHSQC
1
8
1
isotropic
1
15N T2-relaxation-dispersion-CPMG-15NHSQC
3
17
3
isotropic
2
15N T2-relaxation-dispersion-CPMG-15NHSQC
1
18
1
isotropic
2
cross-correlated DD/CSA relaxation-15NHSQC
NMR details
Text: STRUCTURE WAS CALCULATED USING CONSENSUS METHOD (BUCHNER L AND GUENTERT P 2015 STRUCTURE 23, 425-434). 20 INDEPENDENT STRUCTURE CALCULATIONS OF 100 CONFORMERS WERE PERFORMED AND A SET OF ...Text: STRUCTURE WAS CALCULATED USING CONSENSUS METHOD (BUCHNER L AND GUENTERT P 2015 STRUCTURE 23, 425-434). 20 INDEPENDENT STRUCTURE CALCULATIONS OF 100 CONFORMERS WERE PERFORMED AND A SET OF CONSTRAINTS CONSISTENT AMONG 60% OF THE ENSEMBLES WAS COMBINED FOR A FINAL CONSENSUS CALCULATION TO GENERATE THIS ENSEMBLE THE PROTEIN CONTAINS A DYNAMIC REGION WITH RESIDUAL STRUCTURE. DUE TO THE AMBIGUOUS NATURE OF THE CONSTRAINTS AND THE DYNAMIC REGION NO ENERGY REFINEMENT WAS PERFORMED
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Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
Details
solution
1
0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2O
WT_15N_protein
90% H2O/10% D2O
solution
2
0.8 mM [U-13C,15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2O
WT_13C15N_protein
90% H2O/10% D2O
solution
3
0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2O
L151G_mutant_15N_protein
90% H2O/10% D2O
solution
5
0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 0.8 mM [U-13C,15N]-99% UCUUU-SL-RNA, 90% H2O/10% D2O
WT_15N_protein_13C15N_RNAcomplex
90% H2O/10% D2O
1:1 complex of 15N-labeled protein with 13C,15N-labeled RNA.
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.8mM
Polypyrimidine-tract binding protein N-terminal RNA recognition motif
[U-15N]-99%
1
10mM
NaH2PO4/NaOHbuffer
none
1
20mM
sodiumchloride
none
1
0.8mM
Polypyrimidine-tract binding protein N-terminal RNA recognition motif
[U-13C,15N]-99%
2
10mM
NaH2PO4/NaOHbuffer
none
2
20mM
sodiumchloride
none
2
0.8mM
Polypyrimidine-tract binding protein N-terminal RNA recognition motif
[U-15N]-99%
3
10mM
NaH2PO4/NaOHbuffer
none
3
20mM
sodiumchloride
none
3
0.8mM
Polypyrimidine-tract binding protein N-terminal RNA recognition motif
Method: torsion angle dynamics / Software ordinal: 1 Details: The structure was calculated using the CONSENSUS protocol of CYANA due better sample the conformational space consistent with the input data. Unlike in traditional CYANA structure ...Details: The structure was calculated using the CONSENSUS protocol of CYANA due better sample the conformational space consistent with the input data. Unlike in traditional CYANA structure calculations, in CONSENSUS structure calculations the constraint list includes ambiguous restraints. There is no refinement protocol for NMR structures using programs which have realistic energy potentials for ambiguous restraints. In addition the structure includes a highly dynamic structural element (alpha3). Therefore no standard refinement was performed.
NMR representative
Selection criteria: target function
NMR ensemble
Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 2000 / Conformers submitted total number: 20
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