HEADER RNA BINDING PROTEIN 01-OCT-05 2B6G TITLE RNA RECOGNITION BY THE VTS1 SAM DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*GP*GP*CP*UP*CP*UP*GP*GP*CP*AP*GP*CP*UP*UP*UP COMPND 3 *C)-3'; COMPND 4 CHAIN: B; COMPND 5 FRAGMENT: SMAUG RECOGNITION ELEMENT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: VTS1P; COMPND 9 CHAIN: A; COMPND 10 FRAGMENT: SAM DOMAIN; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PRODUCED BY T7 POLYMERASE BASED IN VITRO SOURCE 4 TRANSCRIPTION; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 8 ORGANISM_TAXID: 4932; SOURCE 9 GENE: VTS1P; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS ALPHA-HELIX, PENTALOOP, HAIRPIN, RNA BINDING PROTEIN EXPDTA SOLUTION NMR AUTHOR L.W.DONALDSON,P.E.JOHNSON REVDAT 4 09-MAR-22 2B6G 1 REMARK SEQADV REVDAT 3 24-FEB-09 2B6G 1 VERSN REVDAT 2 21-FEB-06 2B6G 1 JRNL REVDAT 1 24-JAN-06 2B6G 0 JRNL AUTH P.E.JOHNSON,L.W.DONALDSON JRNL TITL RNA RECOGNITION BY THE VTS1P SAM DOMAIN JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 177 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16429155 JRNL DOI 10.1038/NSMB1039 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, XPLOR-NIH 2.11.0 REMARK 3 AUTHORS : GUENTERT (CYANA), SCHWEITERS (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PROTEIN NOE RESTRAINTS WERE CALIBRATED REMARK 3 FROM PEAK VOLUMES TO DISTANCES RANGING FROM 1.8-5.0 USING THE REMARK 3 CANDID MODULE OF CYANA V2.1. INITIALLY, 100 STRUCTURES WERE REMARK 3 CALCULATED WITH XPLOR-NIH V2.11.0 STARTING FROM A PARTIALLY REMARK 3 DOCKED PROTEIN-RNA COMPLEX. A SIMULATED ANNEALING APPROACH WITH REMARK 3 INTERNAL TORSION ANGLE DYNAMICS, DELPHIC DATABASE POTENTIALS AND REMARK 3 RNA PLANARITY RESTRAINTS WAS USED. FROM THE INITIAL ENSEMBLE OF REMARK 3 STRUCTURES, 20 WERE SELECTED BASED UPON LOW ENERGY, NO NOE REMARK 3 VIOLATIONS > 0.5 ANGSTROMS AND NO DIHEDRAL ANGLE VIOLATIONS > 5 REMARK 3 DEGREES. RESTRAINTS USED FOR THE STRUCTURE CALCULATION: 882 REMARK 3 INTRARESIDUE PROTEIN-PROTEIN NOE, 435 SEQUENTIAL PROTEIN-PROTEIN REMARK 3 NOE, 335 MEDIUM RANGE PROTEIN-PROTEIN NOE, 263 LONG RANGE REMARK 3 PROTEIN-PROTEIN NOE, 80 PROTEIN HYDROGEN BONDS, 60 RNA-RNA NOE, REMARK 3 23 PROTEIN-RNA NOE, 140 PROTEIN DIHEDRAL ANGLE, 93 RNA DIHEDRAL REMARK 3 ANGLE. REMARK 4 REMARK 4 2B6G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034733. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.8 REMARK 210 IONIC STRENGTH : 150 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2-0.8 MM U-15N,13C; 20 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH 7.8, REMARK 210 150 MM SODIUM CHLORIDE, 0.02 % REMARK 210 SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 2D NOESY; 2D_ REMARK 210 12C-FILTERED_13C-EDITED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH 2.11.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 GLY A 405 REMARK 465 SER A 406 REMARK 465 ASN A 407 REMARK 465 VAL A 408 REMARK 465 PHE A 409 REMARK 465 ASN A 410 REMARK 465 ASN A 411 REMARK 465 THR A 412 REMARK 465 ILE A 413 REMARK 465 THR A 414 REMARK 465 HIS A 415 REMARK 465 PRO A 416 REMARK 465 ASN A 417 REMARK 465 ALA A 418 REMARK 465 GLY A 419 REMARK 465 PRO A 420 REMARK 465 THR A 421 REMARK 465 SER A 422 REMARK 465 ALA A 423 REMARK 465 THR A 424 REMARK 465 SER A 425 REMARK 465 THR A 426 REMARK 465 SER A 427 REMARK 465 THR A 428 REMARK 465 SER A 429 REMARK 465 SER A 430 REMARK 465 ASN A 431 REMARK 465 GLY A 432 REMARK 465 ASN A 433 REMARK 465 THR A 434 REMARK 465 PRO A 435 REMARK 465 LEU A 436 REMARK 465 SER A 437 REMARK 465 SER A 438 REMARK 465 ASN A 439 REMARK 465 SER A 440 REMARK 465 SER A 441 REMARK 465 MET A 442 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 O2' G B 11 H4' C B 12 1.44 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 ARG A 464 15.55 94.84 REMARK 500 HIS A 466 -19.31 -38.60 REMARK 500 VAL A 493 60.64 31.00 REMARK 500 ALA A 495 110.38 -34.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D3D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UNLIGANDED VTS1 SAM DOMAIN DBREF 2B6G A 407 523 GB 6324935 NP_015004 407 523 DBREF 2B6G B 1 19 PDB 2B6G 2B6G 1 19 SEQADV 2B6G GLY A 405 GB 6324935 CLONING ARTIFACT SEQADV 2B6G SER A 406 GB 6324935 CLONING ARTIFACT SEQRES 1 B 19 G G A G G C U C U G G C A SEQRES 2 B 19 G C U U U C SEQRES 1 A 119 GLY SER ASN VAL PHE ASN ASN THR ILE THR HIS PRO ASN SEQRES 2 A 119 ALA GLY PRO THR SER ALA THR SER THR SER THR SER SER SEQRES 3 A 119 ASN GLY ASN THR PRO LEU SER SER ASN SER SER MET ASN SEQRES 4 A 119 PRO LYS SER LEU THR ASP PRO LYS LEU LEU LYS ASN ILE SEQRES 5 A 119 PRO MET TRP LEU LYS SER LEU ARG LEU HIS LYS TYR SER SEQRES 6 A 119 ASP ALA LEU SER GLY THR PRO TRP ILE GLU LEU ILE TYR SEQRES 7 A 119 LEU ASP ASP GLU THR LEU GLU LYS LYS GLY VAL LEU ALA SEQRES 8 A 119 LEU GLY ALA ARG ARG LYS LEU LEU LYS ALA PHE GLY ILE SEQRES 9 A 119 VAL ILE ASP TYR LYS GLU ARG ASP LEU ILE ASP ARG SER SEQRES 10 A 119 ALA TYR HELIX 1 1 ASN A 443 THR A 448 1 6 HELIX 2 2 ASP A 449 ASN A 455 1 7 HELIX 3 3 ASN A 455 ARG A 464 1 10 HELIX 4 4 LEU A 465 SER A 473 1 9 HELIX 5 5 PRO A 476 ILE A 481 1 6 HELIX 6 6 ASP A 484 GLY A 492 1 9 HELIX 7 7 ALA A 495 ASP A 516 1 22 HELIX 8 8 ASP A 519 TYR A 523 5 5 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