HEADER RNA 21-JAN-05 1YMO TITLE SOLUTION STRUCTURE OF THE P2B-P3 PSEUDOKNOT FROM HUMAN 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 COMPOSED OF COMPND 8 NUCLEOTIDES 95-119 AND 166-183 WITH A U177 DELETION (MATURE HTR RNA COMPND 9 NUMBERING SYSTEM) SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA IS SYNTHESIZED USING IN VITRO TRANSCRIPTION WITH SOURCE 4 T7 RNA POLYMERASE AND A PARTIALLY DOUBLE-STRANDED DNA TEMPLATE. THE SOURCE 5 SEQUENCE OF THIS RNA CAN BE FOUND NATURALLY IN HOMO SAPIENS (HUMAN). KEYWDS PSEUDOKNOT, NON-CANONICAL, TERTIARY STRUCTURE, HOOGSTEEN, TRIPLEX, KEYWDS 2 RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.A.THEIMER,C.A.BLOIS,J.FEIGON REVDAT 4 29-NOV-23 1YMO 1 REMARK REVDAT 3 02-MAR-22 1YMO 1 REMARK 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 REVEALS JRNL TITL 2 CONSERVED TERTIARY INTERACTIONS ESSENTIAL 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 CHANGES IN REMARK 1 TITL 2 THE STRUCTURAL EQUILIBRIUM IN 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 CONGENITA REMARK 1 TITL 2 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 : XWINNMR 2.6, XPLOR-NIH 1.0.6 REMARK 3 AUTHORS : BRUKER (XWINNMR), NIH (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 790 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 210 DIHEDRAL ANGLE RESTRAINTS, 50 DISTANCE REMARK 3 RESTRAINTS FROM HYDROGEN BONDS, AND 20 H-C RESIDUAL DIPOLAR REMARK 3 COUPLINGS. PDB ENTRY PDB ENTRY 2K96 IS A BETTER REFINED REMARK 3 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 DEPOSITION ID IS D_1000031691. 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 6.3, REMARK 210 200 MM KCL, 50 UM EDTA, 0.2% REMARK 210 SODIUM AZIDE, 95% H2O,5% D2O OR REMARK 210 100% D2O; ~0.8 MM 13C,15N-FULLY REMARK 210 LABELED RNA, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, PH 6.3, 200 MM REMARK 210 KCL, 50 UM EDTA, 0.2% SODIUM REMARK 210 AZIDE, 95% H2O,5% D2O OR 100% REMARK 210 D2O; ~0.8 MM 13C,15N-A LABELED REMARK 210 RNA, 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER, PH 6.3, 200 MM KCL, 50 REMARK 210 UM EDTA, 0.2% SODIUM AZIDE , 95% REMARK 210 H2O,5% D2O OR 100% D2O; ~0.8 MM REMARK 210 13C,15N-C LABELED RNA, 10 MM REMARK 210 SODIUM PHOSPHATE BUFFER, PH 6.3, REMARK 210 200 MM KCL, 50 UM EDTA, 0.2% REMARK 210 SODIUM AZIDE, 95% H2O,5% D2O OR REMARK 210 100% D2O; ~0.8 MM 13C,15N-G REMARK 210 LABELED RNA, 10 MM SODIUM REMARK 210 PHOSPHATE BUFFER, PH 6.3, 200 MM REMARK 210 KCL, 50 UM EDTA, 0.2% SODIUM REMARK 210 AZIDE, 95% H2O,5% D2O OR 100% REMARK 210 D2O; ~0.8 MM 13C,15N-U LABELED REMARK 210 RNA, 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER, PH 6.3, 200 MM KCL, 50 REMARK 210 UM EDTA, 0.2% SODIUM AZIDE, 95% REMARK 210 H2O,5% D2O OR 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY (11ECHO AND WATERGATE); REMARK 210 2D NOESY, 2D TOCSY (PRESAT); 2D REMARK 210 15N-HMQC,2D 15N-CPMG-NOESY, 2D REMARK 210 JNN-HNN-COSY; 2D 13C-HSQC; 2D REMARK 210 13C-HSQC, 2D HCCH COSY, 3D HCCH- REMARK 210 TOCSY, 2D 13C FILTERED/EDITED REMARK 210 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 VIOLATIONS, REMARK 210 CONSISTENT WITH RESIDUAL DIPOLAR REMARK 210 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 SINGLY REMARK 210 -LABELED SAMPLES EXCEPT FOR RESIDUAL DIPOLAR COUPLINGS WHICH REMARK 210 WERE ONLY COLLECTED FOR THE A- AND G-ONLY LABELED 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 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: 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 O4 U A 13 H42 C A 46 1.42 REMARK 500 O2 U A 5 H62 A A 35 1.43 REMARK 500 O2' A A 35 H8 A A 36 1.47 REMARK 500 HO2' A A 31 O4' A A 32 1.48 REMARK 500 H5'' G A 6 OP1 U A 7 1.57 REMARK 500 O2' C A 27 H6 C A 28 1.58 REMARK 500 O2' G A 2 H8 G A 3 1.58 REMARK 500 O2' A A 39 H8 A A 40 1.58 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. = -2.6 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: PDB REMARK 900 SOLUTION STRUCTURE OF THE WILDTYPE P2B HAIRPIN FROM HUMAN REMARK 900 TELOMERASE RNA REMARK 900 RELATED ID: 1Q75 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE DYSKERATOSIS CONGENITA MUTANT P2B HAIRPIN REMARK 900 FROM HUMAN TELOMERASE RNA REMARK 900 RELATED ID: 2K96 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF P2B-P3 PSEUDOKNOT MUTANT OF HUMAN TELOMERASE REMARK 900 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 MODEL 1