HEADER RNA 21-JAN-05 1YMO TITLE SOLUTION STRUCTURE OF THE P2B-P3 PSEUDOKNOT FROM HUMAN TITLE 2 TELOMERASE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERASE RNA P2B-P3 PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P2B-P3 PSEUDOKNOT; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: A UNIMOLECULAR PSEUDOKNOT CONSTRUCT COMPND 8 COMPOSED OF NUCLEOTIDES 95-119 AND 166-183 WITH A U177 COMPND 9 DELETION (MATURE HTR RNA NUMBERING SYSTEM) SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA IS SYNTHESIZED USING IN VITRO SOURCE 4 TRANSCRIPTION WITH T7 RNA POLYMERASE AND A PARTIALLY SOURCE 5 DOUBLE-STRANDED DNA TEMPLATE. THE SEQUENCE OF THIS RNA CAN SOURCE 6 BE FOUND NATURALLY IN HOMO SAPIENS (HUMAN). KEYWDS PSEUDOKNOT, NON-CANONICAL, TERTIARY STRUCTURE, HOOGSTEEN, KEYWDS 2 TRIPLEX, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.A.THEIMER,C.A.BLOIS,J.FEIGON REVDAT 2 24-FEB-09 1YMO 1 VERSN REVDAT 1 15-MAR-05 1YMO 0 JRNL AUTH C.A.THEIMER,C.A.BLOIS,J.FEIGON JRNL TITL STRUCTURE OF THE HUMAN TELOMERASE RNA PSEUDOKNOT JRNL TITL 2 REVEALS CONSERVED TERTIARY INTERACTIONS ESSENTIAL JRNL TITL 3 FOR FUNCTION JRNL REF MOL.CELL V. 17 671 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 15749017 JRNL DOI 10.1016/J.MOLCEL.2005.01.017 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.THEIMER,L.D.FINGER,L.TRANTIREK,J.FEIGON REMARK 1 TITL MUTATIONS LINKED TO DYSKERATOSIS CONGENITA CAUSE REMARK 1 TITL 2 CHANGES IN THE STRUCTURAL EQUILIBRIUM IN REMARK 1 TITL 3 TELOMERASE RNA REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 100 449 2003 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.A.THEIMER,L.D.FINGER,J.FEIGON REMARK 1 TITL YNMG TETRALOOP FORMATION BY A DYSKERATOSIS REMARK 1 TITL 2 CONGENITA MUTATION IN HUMAN TELOMERASE RNA REMARK 1 REF RNA V. 9 1446 2003 REMARK 1 REFN ISSN 1355-8382 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 1.0.6 REMARK 3 AUTHORS : NIH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 790 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS, 210 DIHEDRAL ANGLE RESTRAINTS, REMARK 3 50 DISTANCE RESTRAINTS FROM HYDROGEN BONDS, AND 20 H-C REMARK 3 RESIDUAL DIPOLAR COUPLINGS. PDB ENTRY PDB ENTRY 2K96 IS A REMARK 3 BETTER REFINED STRUCTURE OF ENTRY 1YMO. REMARK 4 REMARK 4 1YMO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031691. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 293 REMARK 210 PH : 6.3; 6.3 REMARK 210 IONIC STRENGTH : 200 MM KCL; 200 MM KCL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : ~0.8 MM UNLABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 6.3, 200 MM KCL, 50 UM EDTA, REMARK 210 0.2% SODIUM AZIDE, 95% H2O,5% REMARK 210 D2O OR 100% D2O; ~0.8 MM 13C, REMARK 210 15N-FULLY LABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 6.3, 200 MM KCL, 50 UM EDTA, REMARK 210 0.2% SODIUM AZIDE, 95% H2O,5% REMARK 210 D2O OR 100% D2O; ~0.8 MM 13C, REMARK 210 15N-A LABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 6.3, 200 MM KCL, 50 UM EDTA, REMARK 210 0.2% SODIUM AZIDE , 95% H2O,5% REMARK 210 D2O OR 100% D2O; ~0.8 MM 13C, REMARK 210 15N-C LABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 6.3, 200 MM KCL, 50 UM EDTA, REMARK 210 0.2% SODIUM AZIDE, 95% H2O,5% REMARK 210 D2O OR 100% D2O; ~0.8 MM 13C, REMARK 210 15N-G LABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 6.3, 200 MM KCL, 50 UM EDTA, REMARK 210 0.2% SODIUM AZIDE, 95% H2O,5% REMARK 210 D2O OR 100% D2O; ~0.8 MM 13C, REMARK 210 15N-U LABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH REMARK 210 6.3, 200 MM KCL, 50 UM EDTA, REMARK 210 0.2% SODIUM AZIDE, 95% H2O,5% REMARK 210 D2O OR 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY (11ECHO AND REMARK 210 WATERGATE), 2D NOESY, 2D TOCSY REMARK 210 (PRESAT), 2D 15N-HMQC,2D 15N- REMARK 210 CPMG-NOESY, 2D JNN-HNN-COSY, REMARK 210 2D 13C-HSQC, 2D 13C-HSQC, 2D REMARK 210 HCCH COSY, 3D HCCH-TOCSY, 2D REMARK 210 13C FILTERED/EDITED NOESYS REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX, AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, AURELIA 3.108, REMARK 210 XPLOR-NIH 1.0.6 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, NO RESTRAINT REMARK 210 VIOLATIONS, CONSISTENT WITH REMARK 210 RESIDUAL DIPOLAR COUPLINGS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE SAME EXPERIMENTS WERE PERFORMED ON ALL OF THE REMARK 210 SINGLY-LABELED SAMPLES EXCEPT FOR RESIDUAL DIPOLAR COUPLINGS REMARK 210 WHICH WERE ONLY COLLECTED FOR THE A- AND G-ONLY LABELED REMARK 210 SAMPLES. 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 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' A A 38 O4' A A 39 2.19 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 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 31 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 32 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 33 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 35 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 36 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 37 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 38 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 39 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 40 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 41 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 41 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 44 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 45 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 45 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 47 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 31 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 32 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 33 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 623 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NA2 RELATED DB: NDB REMARK 900 SOLUTION STRUCTURE OF THE WILDTYPE P2B HAIRPIN FROM HUMAN REMARK 900 TELOMERASE RNA REMARK 900 RELATED ID: 1Q75 RELATED DB: NDB REMARK 900 SOLUTION STRUCTURE OF THE DYSKERATOSIS CONGENITA MUTANT P2B REMARK 900 HAIRPIN FROM HUMAN TELOMERASE RNA REMARK 900 RELATED ID: 2K96 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF P2B-P3 PSEUDOKNOT MUTANT OF HUMAN REMARK 900 TELOMERASE RNA DBREF 1YMO A 1 47 PDB 1YMO 1YMO 1 47 SEQRES 1 A 47 G G G C U G U U U U U C U SEQRES 2 A 47 C G C U G A C U U U C A G SEQRES 3 A 47 C C C C A A A C A A A A A SEQRES 4 A 47 A G U C A G C A 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 195 0 0 0 0 0 0 6 0 0 0 4 END