HEADER RNA BINDING PROTEIN 27-OCT-22 8BGF TITLE NMR SOLUTION STRUCTURE OF THE N-TERMINAL RRM AND FLANKING LINKER TITLE 2 REGIONS OF POLYPYRIMIDINE TRACT BINDING PROTEIN 1 USING THE CYANA TITLE 3 CONSENSUS METHOD. COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PTB,57 KDA RNA-BINDING PROTEIN PPTB-1,HETEROGENEOUS NUCLEAR COMPND 5 RIBONUCLEOPROTEIN I,HNRNP I; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTBP1, PTB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON-PLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB11 KEYWDS RNA BINDING PROTEIN ALTERNATIVE SPLICING REPRESSOR IRES TRANS-ACTING KEYWDS 2 FACTOR RNA RECOGNITION MOTIF DYNAMIC STRUCTURE, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.D.DAMBERGER,I.BEUSCH,F.H.-T.ALLAIN REVDAT 1 08-NOV-23 8BGF 0 JRNL AUTH F.DAMBERGER,M.KREPL,I.BEUSCH,G.DORN,C.MARIS,J.SPONER, JRNL AUTH 2 S.RAVINDRANATHAN,F.H.-T.ALLAIN JRNL TITL N-TERMINAL DOMAIN OF POLYPYRIMIDINE-TRACT BINDING PROTEIN IS JRNL TITL 2 A DYNAMIC FOLDING PLATFORM FOR ADAPTIVE RNA RECOGNITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.MARIS,S.JAYNE,F.F.DAMBERGER,I.BEUSCH,G.DORN, REMARK 1 AUTH 2 S.RAVINDRANATHAN,F.H.ALLAIN REMARK 1 TITL A TRANSIENT ALPHA-HELIX IN THE N-TERMINAL RNA RECOGNITION REMARK 1 TITL 2 MOTIF OF POLYPYRIMIDINE TRACT BINDING PROTEIN SENSES RNA REMARK 1 TITL 3 SECONDARY STRUCTURE. REMARK 1 REF NUCLEIC ACIDS RES V. 48 4521 2020 REMARK 1 REFN ESSN 1362-4962 REMARK 1 PMID 32170319 REMARK 1 DOI 10.1093/NAR/GKAA155 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.97BETA, CYANA 3.97BETA REMARK 3 AUTHORS : GUNTERT & BUCHNER (CYANA), GUNTERT & BUCHNER REMARK 3 (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS CALCULATED USING THE REMARK 3 CONSENSUS PROTOCOL OF CYANA DUE BETTER SAMPLE THE CONFORMATIONAL REMARK 3 SPACE CONSISTENT WITH THE INPUT DATA. UNLIKE IN TRADITIONAL REMARK 3 CYANA STRUCTURE CALCULATIONS, IN CONSENSUS STRUCTURE REMARK 3 CALCULATIONS THE CONSTRAINT LIST INCLUDES AMBIGUOUS RESTRAINTS. REMARK 3 THERE IS NO REFINEMENT PROTOCOL FOR NMR STRUCTURES USING REMARK 3 PROGRAMS WHICH HAVE REALISTIC ENERGY POTENTIALS FOR AMBIGUOUS REMARK 3 RESTRAINTS. IN ADDITION THE STRUCTURE INCLUDES A HIGHLY DYNAMIC REMARK 3 STRUCTURAL ELEMENT (ALPHA3). THEREFORE NO STANDARD REFINEMENT REMARK 3 WAS PERFORMED. REMARK 4 REMARK 4 8BGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126017. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313; 298; 293 REMARK 210 PH : 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 33.3; 33.3; 33.3 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-15N]-99% REMARK 210 POLYPYRIMIDINE-TRACT BINDING REMARK 210 PROTEIN N-TERMINAL RNA REMARK 210 RECOGNITION MOTIF, 10 MM NAH2PO4/ REMARK 210 NAOH BUFFER, 20 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-13C,15N]-99% REMARK 210 POLYPYRIMIDINE-TRACT BINDING REMARK 210 PROTEIN N-TERMINAL RNA REMARK 210 RECOGNITION MOTIF, 10 MM NAH2PO4/ REMARK 210 NAOH BUFFER, 20 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-15N]-99% POLYPYRIMIDINE- REMARK 210 TRACT BINDING PROTEIN N-TERMINAL REMARK 210 RNA RECOGNITION MOTIF, 10 MM REMARK 210 NAH2PO4/NAOH BUFFER, 20 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 0.8 MM [U-15N]-99% REMARK 210 POLYPYRIMIDINE-TRACT BINDING REMARK 210 PROTEIN N-TERMINAL RNA REMARK 210 RECOGNITION MOTIF, 10 MM NAH2PO4/ REMARK 210 NAOH BUFFER, 20 MM SODIUM REMARK 210 CHLORIDE, 0.8 MM [U-13C,15N]-99% REMARK 210 UCUUU-SL-RNA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 15N T1-RELAXATION-15HSQC; 15N T2-RELAXATION-T1RHO-15NHSQC; REMARK 210 {1H}15N-NOE-15NHSQC; RELAXATION-COMPENSATED IZNZ REX HSQC; 15N REMARK 210 T2-RELAXATION-DISPERSION CPMG-15NHSQC; 15N T2-RELAXATION- REMARK 210 DISPERSION-CPMG-15NHSQC; CROSS-CORRELATED DD/CSA RELAXATION- REMARK 210 15NHSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 750 MHZ; 700 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3, CARA 1.9.1.7, CYANA REMARK 210 3.97BETA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 2000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STRUCTURE WAS CALCULATED USING CONSENSUS METHOD REMARK 210 (BUCHNER L AND GUENTERT P 2015 STRUCTURE 23, 425-434). REMARK 210 20 INDEPENDENT STRUCTURE CALCULATIONS OF 100 CONFORMERS REMARK 210 WERE PERFORMED AND A SET OF CONSTRAINTS CONSISTENT AMONG REMARK 210 60% OF THE ENSEMBLES WAS COMBINED FOR A FINAL CONSENSUS REMARK 210 CALCULATION TO GENERATE THIS ENSEMBLE REMARK 210 THE PROTEIN CONTAINS A DYNAMIC REGION WITH RESIDUAL STRUCTURE. REMARK 210 DUE TO THE AMBIGUOUS NATURE OF THE CONSTRAINTS AND THE DYNAMIC REMARK 210 REGION NO ENERGY REFINEMENT WAS PERFORMED REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ASP A 43 138.90 -171.87 REMARK 500 1 LYS A 45 87.70 55.97 REMARK 500 1 PHE A 47 91.11 62.37 REMARK 500 1 ASP A 50 -52.55 -128.79 REMARK 500 1 PRO A 57 77.12 -69.74 REMARK 500 1 LEU A 88 105.09 -170.27 REMARK 500 1 VAL A 117 -164.78 -101.13 REMARK 500 1 PRO A 119 80.02 -69.79 REMARK 500 1 GLN A 129 138.09 -172.78 REMARK 500 1 GLU A 135 88.15 -179.50 REMARK 500 1 SER A 140 82.06 57.90 REMARK 500 1 ASN A 143 38.80 -99.40 REMARK 500 1 GLN A 144 -40.41 -131.95 REMARK 500 1 ARG A 146 44.81 -92.43 REMARK 500 1 ALA A 147 -42.97 -134.66 REMARK 500 1 GLN A 158 -48.38 -150.55 REMARK 500 1 SER A 159 -173.04 59.10 REMARK 500 1 LEU A 162 89.73 55.37 REMARK 500 2 SER A 44 82.19 54.51 REMARK 500 2 LYS A 45 79.21 -159.18 REMARK 500 2 LYS A 46 -54.00 -146.44 REMARK 500 2 SER A 51 -62.34 -106.67 REMARK 500 2 ARG A 52 -169.92 59.16 REMARK 500 2 SER A 53 -173.48 63.20 REMARK 500 2 PRO A 57 77.18 -69.79 REMARK 500 2 LEU A 88 103.35 -163.13 REMARK 500 2 LEU A 91 56.98 -111.84 REMARK 500 2 VAL A 117 -164.78 -100.94 REMARK 500 2 PRO A 119 80.17 -69.77 REMARK 500 2 GLN A 129 137.35 -171.09 REMARK 500 2 GLU A 135 64.18 -176.48 REMARK 500 2 ASP A 139 -169.80 -116.02 REMARK 500 2 PRO A 142 73.62 -69.77 REMARK 500 2 ASN A 143 -36.00 179.20 REMARK 500 2 ALA A 149 -48.18 -158.63 REMARK 500 2 LEU A 162 -175.69 59.32 REMARK 500 3 LYS A 46 -56.71 -123.92 REMARK 500 3 PHE A 47 72.64 55.20 REMARK 500 3 ARG A 52 83.44 53.62 REMARK 500 3 SER A 53 -74.29 -74.97 REMARK 500 3 ALA A 54 67.96 -177.57 REMARK 500 3 PRO A 57 77.08 -69.74 REMARK 500 3 PRO A 119 80.55 -69.73 REMARK 500 3 ASP A 139 48.14 -179.18 REMARK 500 3 SER A 140 60.79 -171.11 REMARK 500 3 GLN A 148 48.27 -90.06 REMARK 500 3 ALA A 149 -69.87 -125.30 REMARK 500 3 ASN A 155 75.49 -111.51 REMARK 500 3 GLN A 158 -72.41 -161.93 REMARK 500 3 ASN A 161 178.89 60.87 REMARK 500 REMARK 500 THIS ENTRY HAS 315 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2N3O RELATED DB: PDB REMARK 900 STRUCTURE OF THE CORRESPONDING CONSTRUCT WHEN BOUTN TO A STEMLOOP REMARK 900 RNA. THIS DEPOSIT OF THE FREE PROTEIN DOCUMENTS RELAXATION REMARK 900 EXPERIMENTS PERFORMED ON BOTH THE FREE AND BOUND PROTEIN. REMARK 900 RELATED ID: 25652 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS FOR THE CONSTRUCT WHEN BOUND TO A STEMLOOP RNA. REMARK 900 RELATED ID: 34766 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE N-TERMINAL RRM AND FLANKING LINKER REMARK 900 REGIONS OF POLYPYRIMIDINE TRACT BINDING PROTEIN 1 USING THE CYANA REMARK 900 CONSENSUS METHOD. DBREF 8BGF A 41 163 UNP P26599 PTBP1_HUMAN 41 163 SEQRES 1 A 123 GLY ASN ASP SER LYS LYS PHE LYS GLY ASP SER ARG SER SEQRES 2 A 123 ALA GLY VAL PRO SER ARG VAL ILE HIS ILE ARG LYS LEU SEQRES 3 A 123 PRO ILE ASP VAL THR GLU GLY GLU VAL ILE SER LEU GLY SEQRES 4 A 123 LEU PRO PHE GLY LYS VAL THR ASN LEU LEU MET LEU LYS SEQRES 5 A 123 GLY LYS ASN GLN ALA PHE ILE GLU MET ASN THR GLU GLU SEQRES 6 A 123 ALA ALA ASN THR MET VAL ASN TYR TYR THR SER VAL THR SEQRES 7 A 123 PRO VAL LEU ARG GLY GLN PRO ILE TYR ILE GLN PHE SER SEQRES 8 A 123 ASN HIS LYS GLU LEU LYS THR ASP SER SER PRO ASN GLN SEQRES 9 A 123 ALA ARG ALA GLN ALA ALA LEU GLN ALA VAL ASN SER VAL SEQRES 10 A 123 GLN SER GLY ASN LEU ALA HELIX 1 AA1 THR A 71 LEU A 78 1 8 HELIX 2 AA2 LEU A 91 ASN A 95 5 5 HELIX 3 AA3 THR A 103 THR A 115 1 13 HELIX 4 AA4 GLN A 144 SER A 156 1 13 SHEET 1 AA1 3 ALA A 97 GLU A 100 0 SHEET 2 AA1 3 VAL A 60 ARG A 64 -1 N ILE A 63 O ALA A 97 SHEET 3 AA1 3 TYR A 127 PHE A 130 -1 O GLN A 129 N HIS A 62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1