HEADER RNA BINDING PROTEIN 19-MAY-17 5O1T TITLE SOLUTION STRUCTURE OF THE RNA BINDING DOMAIN OF NRD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NRD1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: NRD1, YNL251C, N0868; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NRD1, RRM, RNA-BINDING, TRANSCRIPTION NON-CODING RNAS, RNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.MARTINEZ-LUMBRERAS,J.M.PEREZ-CANADILLAS REVDAT 4 14-JUN-23 5O1T 1 REMARK REVDAT 3 08-MAY-19 5O1T 1 REMARK REVDAT 2 11-OCT-17 5O1T 1 JRNL REVDAT 1 02-AUG-17 5O1T 0 JRNL AUTH E.FRANCO-ECHEVARRIA,N.GONZALEZ-POLO,S.ZORRILLA, JRNL AUTH 2 S.MARTINEZ-LUMBRERAS,C.M.SANTIVERI,R.CAMPOS-OLIVAS, JRNL AUTH 3 M.SANCHEZ,O.CALVO,B.GONZALEZ,J.M.PEREZ-CANADILLAS JRNL TITL THE STRUCTURE OF TRANSCRIPTION TERMINATION FACTOR NRD1 JRNL TITL 2 REVEALS AN ORIGINAL MODE FOR GUAA RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 45 10293 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28973465 JRNL DOI 10.1093/NAR/GKX685 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200004990. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 59.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 600 UM [U-100% 13C; U-100% 15N] REMARK 210 NRD1, 25 MM POTASSIUM PHOSPHATE, REMARK 210 25 MM SODIUM CHLORIDE, 1 MM DTT, REMARK 210 90% H2O/10% D2O; 800 UM NRD1, 25 REMARK 210 MM POTASSIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 1 MM DTT, 90% REMARK 210 H2O/10% D2O; 400 UM [U-100% 13C; REMARK 210 U-100% 15N] EXPECT FOR PHE AND REMARK 210 LEU RESIDUES NRD1, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 1 MM DTT, 90% REMARK 210 H2O/10% D2O; 400 UM [U-100% 13C; REMARK 210 U-100% 15N] EXPECT FOR ILE REMARK 210 RESIDUES NRD1, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 1 MM DTT, 90% H2O/10% D2O; 400 REMARK 210 UM [U-100% 13C; U-100% 15N] REMARK 210 EXPECT FOR ARG RESIDUES NRD1, 25 REMARK 210 MM POTASSIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 1 MM DTT, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HNCO; 3D CBCA(CO)NH; REMARK 210 3D HCCH-TOCSY; 2D 1H-1H NOESY; REMARK 210 3D 1H-15N NOESY; 2D 1H-1H NOESY REMARK 210 F1FILTERED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, CCPNMR REMARK 210 ANALYSIS, CYANA REMARK 210 METHOD USED : MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ARG A 339 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 12 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 12 ARG A 384 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 15 ARG A 429 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 19 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 20 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 PRO A 294 -79.81 -66.75 REMARK 500 1 ASN A 295 -31.15 -178.20 REMARK 500 1 THR A 297 -30.37 -169.99 REMARK 500 1 PHE A 298 -156.03 58.07 REMARK 500 1 ASN A 301 -73.51 -109.54 REMARK 500 1 HIS A 303 22.14 -79.79 REMARK 500 1 PRO A 307 -158.05 -71.36 REMARK 500 1 GLU A 309 -150.04 41.12 REMARK 500 1 LYS A 321 79.41 -110.38 REMARK 500 1 ILE A 462 50.19 -108.09 REMARK 500 1 ILE A 463 -179.09 -57.87 REMARK 500 1 VAL A 464 -48.31 -150.74 REMARK 500 1 GLU A 466 -163.62 62.86 REMARK 500 2 ALA A 293 168.40 70.25 REMARK 500 2 PRO A 294 -155.45 -73.23 REMARK 500 2 THR A 296 27.18 46.70 REMARK 500 2 THR A 300 -146.65 -134.86 REMARK 500 2 ASN A 302 163.47 69.30 REMARK 500 2 PRO A 307 -158.58 -71.91 REMARK 500 2 ILE A 462 53.19 -99.56 REMARK 500 2 ILE A 463 -178.42 -61.74 REMARK 500 2 VAL A 464 -48.86 -154.99 REMARK 500 2 GLU A 466 165.66 76.23 REMARK 500 3 PRO A 294 -164.19 -66.98 REMARK 500 3 ASN A 301 -73.50 -105.73 REMARK 500 3 ASN A 302 166.79 177.99 REMARK 500 3 ASP A 308 -66.76 71.12 REMARK 500 3 GLU A 309 -172.79 44.50 REMARK 500 3 ILE A 462 48.68 -107.37 REMARK 500 3 VAL A 464 -47.26 -139.57 REMARK 500 4 THR A 297 -35.20 -172.82 REMARK 500 4 ASN A 301 -38.53 176.55 REMARK 500 4 HIS A 303 15.05 -143.29 REMARK 500 4 PRO A 307 -169.87 -68.82 REMARK 500 4 LYS A 321 79.40 -110.17 REMARK 500 4 ILE A 462 48.94 -103.97 REMARK 500 4 VAL A 464 -54.96 -140.29 REMARK 500 5 PRO A 294 -157.57 -72.50 REMARK 500 5 THR A 296 26.65 48.66 REMARK 500 5 HIS A 303 9.88 -151.68 REMARK 500 5 ILE A 463 171.31 -59.62 REMARK 500 5 VAL A 464 -58.46 -139.27 REMARK 500 6 ILE A 291 75.18 69.10 REMARK 500 6 PRO A 294 -158.31 -75.55 REMARK 500 6 THR A 296 48.50 -81.01 REMARK 500 6 THR A 300 -76.23 -117.02 REMARK 500 6 ASN A 301 -52.94 -164.85 REMARK 500 6 ILE A 462 55.06 -90.65 REMARK 500 6 ILE A 463 -176.60 -64.81 REMARK 500 6 VAL A 464 -49.72 -160.61 REMARK 500 REMARK 500 THIS ENTRY HAS 168 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 462 ILE A 463 1 142.72 REMARK 500 ILE A 462 ILE A 463 2 141.74 REMARK 500 ILE A 462 ILE A 463 3 137.87 REMARK 500 ILE A 462 ILE A 463 4 138.75 REMARK 500 ILE A 462 ILE A 463 5 137.93 REMARK 500 ILE A 462 ILE A 463 6 146.83 REMARK 500 ILE A 462 ILE A 463 7 141.47 REMARK 500 ILE A 462 ILE A 463 8 141.12 REMARK 500 ILE A 462 ILE A 463 9 139.46 REMARK 500 ILE A 462 ILE A 463 10 135.26 REMARK 500 ILE A 462 ILE A 463 11 138.69 REMARK 500 ILE A 462 ILE A 463 12 140.62 REMARK 500 ILE A 462 ILE A 463 13 137.74 REMARK 500 ILE A 462 ILE A 463 14 143.13 REMARK 500 ILE A 462 ILE A 463 15 140.41 REMARK 500 ILE A 462 ILE A 463 16 140.53 REMARK 500 ILE A 462 ILE A 463 17 141.04 REMARK 500 ILE A 462 ILE A 463 18 140.56 REMARK 500 ILE A 462 ILE A 463 19 138.26 REMARK 500 ILE A 462 ILE A 463 20 142.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 ARG A 339 0.08 SIDE CHAIN REMARK 500 12 ARG A 339 0.08 SIDE CHAIN REMARK 500 13 ARG A 319 0.07 SIDE CHAIN REMARK 500 15 TYR A 422 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34140 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE RNA BINDING DOMAIN OF NRD1 DBREF 5O1T A 290 468 UNP P53617 NRD1_YEAST 290 468 SEQRES 1 A 179 SER ILE GLY ALA PRO ASN THR THR PHE GLY THR ASN ASN SEQRES 2 A 179 HIS HIS LEU TYR PRO ASP GLU LEU ASN VAL SER ASN ASN SEQRES 3 A 179 PRO HIS TYR ARG PRO LYS PRO VAL SER TYR ASP SER THR SEQRES 4 A 179 LEU PRO PRO ASP HIS ILE LYS VAL TYR SER ARG THR LEU SEQRES 5 A 179 PHE ILE GLY GLY VAL PRO LEU ASN MET LYS GLU TRP ASP SEQRES 6 A 179 LEU ALA ASN VAL LEU LYS PRO PHE ALA GLU VAL GLN SER SEQRES 7 A 179 VAL ILE LEU ASN ASN SER ARG LYS HIS ALA PHE VAL LYS SEQRES 8 A 179 VAL TYR SER ARG HIS GLU ALA GLU ASN VAL LEU GLN ASN SEQRES 9 A 179 PHE ASN LYS ASP GLY ALA LEU PRO LEU ARG THR ARG TRP SEQRES 10 A 179 GLY VAL GLY PHE GLY PRO ARG ASP CYS CYS ASP TYR GLN SEQRES 11 A 179 HIS GLY TYR SER ILE ILE PRO MET HIS ARG LEU THR ASP SEQRES 12 A 179 ALA ASP LYS LYS TRP SER VAL SER ALA GLN TRP GLY GLY SEQRES 13 A 179 THR SER GLY GLN PRO LEU VAL THR GLY ILE VAL PHE GLU SEQRES 14 A 179 GLU PRO ASP ILE ILE VAL GLY GLU GLY VAL HELIX 1 AA1 THR A 296 THR A 300 5 5 HELIX 2 AA2 LYS A 351 LYS A 360 1 10 HELIX 3 AA3 ASN A 372 LYS A 375 5 4 HELIX 4 AA4 SER A 383 PHE A 394 1 12 HELIX 5 AA5 PRO A 412 ASP A 414 5 3 HELIX 6 AA6 HIS A 428 LEU A 430 5 3 HELIX 7 AA7 THR A 431 ALA A 441 1 11 SHEET 1 AA1 5 SER A 324 TYR A 325 0 SHEET 2 AA1 5 ILE A 455 GLU A 458 -1 O VAL A 456 N SER A 324 SHEET 3 AA1 5 HIS A 333 TYR A 337 1 N TYR A 337 O PHE A 457 SHEET 4 AA1 5 TYR A 422 PRO A 426 -1 O SER A 423 N VAL A 336 SHEET 5 AA1 5 CYS A 416 ASP A 417 -1 N ASP A 417 O TYR A 422 SHEET 1 AA2 4 VAL A 365 ASN A 371 0 SHEET 2 AA2 4 HIS A 376 VAL A 381 -1 O HIS A 376 N ASN A 371 SHEET 3 AA2 4 THR A 340 GLY A 344 -1 N ILE A 343 O ALA A 377 SHEET 4 AA2 4 ARG A 403 TRP A 406 -1 O ARG A 405 N PHE A 342 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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