HEADER RNA 29-SEP-08 2K95 TITLE SOLUTION STRUCTURE OF THE WILD-TYPE P2B-P3 PSEUDOKNOT OF HUMAN TITLE 2 TELOMERASE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TELOMERASE RNA P2B-P3 PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WILD-TYPE P2B-P3 PSEUDOKNOT; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TELOMERASE, RNA, PSEUDOKNOT, TRIPLE HELIX, BULGE, RDC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.-K.KIM,Q.ZHANG,J.ZHOU,C.A.THEIMER,R.D.PETERSON,J.FEIGON REVDAT 5 16-MAR-22 2K95 1 REMARK REVDAT 4 09-JUN-09 2K95 1 REVDAT REVDAT 3 24-FEB-09 2K95 1 VERSN REVDAT 2 16-DEC-08 2K95 1 JRNL REVDAT 1 25-NOV-08 2K95 0 JRNL AUTH N.K.KIM,Q.ZHANG,J.ZHOU,C.A.THEIMER,R.D.PETERSON,J.FEIGON JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF THE WILD-TYPE PSEUDOKNOT JRNL TITL 2 OF HUMAN TELOMERASE RNA. JRNL REF J.MOL.BIOL. V. 384 1249 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18950640 JRNL DOI 10.1016/J.JMB.2008.10.005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.9.8, X-PLOR NIH 2.9.8 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K95 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000100832. 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 : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM PKWT, 10 MM SODIUM REMARK 210 PHOSPHATE, 200 MM POTASSIUM REMARK 210 CHLORIDE, 50 UM EDTA, 95 % H2O, REMARK 210 5 % D2O; 1 MM PKWT, 10 MM SODIUM REMARK 210 PHOSPHATE, 200 MM POTASSIUM REMARK 210 CHLORIDE, 50 UM EDTA, 100 % D2O; REMARK 210 1 MM [U-98% 13C; U-98% 15N] PKWT, REMARK 210 10 MM SODIUM PHOSPHATE, 200 MM REMARK 210 POTASSIUM CHLORIDE, 50 UM EDTA, REMARK 210 95 % H2O, 5 % D2O; 1 MM [U-98% REMARK 210 13C; U-98% 15N] PKWT, 10 MM REMARK 210 SODIUM PHOSPHATE, 200 MM REMARK 210 POTASSIUM CHLORIDE, 50 UM EDTA, REMARK 210 100 % D2O; 1 MM [U-13C; U-15N]- REMARK 210 ADE, [U-13C; U-15N]-URA PKWT, 10 REMARK 210 MM SODIUM PHOSPHATE, 200 MM REMARK 210 POTASSIUM CHLORIDE, 50 UM EDTA, REMARK 210 95 % H2O, 5 % D2O, 0.2 % SODIUM REMARK 210 AZIDE; 1 MM [U-13C; U-15N]-ADE, REMARK 210 [U-13C; U-15N]-URA PKWT, 10 MM REMARK 210 SODIUM PHOSPHATE, 200 MM REMARK 210 POTASSIUM CHLORIDE, 50 UM EDTA, REMARK 210 100 % D2O, 0.2 % SODIUM AZIDE; 1 REMARK 210 MM [U-13C; U-15N]-GUA, [U-13C; U- REMARK 210 15N]-CYT PKWT, 10 MM SODIUM REMARK 210 PHOSPHATE, 200 MM POTASSIUM REMARK 210 CHLORIDE, 50 UM EDTA, 95 % H2O, REMARK 210 5 % D2O, 0.2 % SODIUM AZIDE; 1 REMARK 210 MM [U-13C; U-15N]-GUA, [U-13C; U- REMARK 210 15N]-CYT PKWT, 10 MM SODIUM REMARK 210 PHOSPHATE, 200 MM POTASSIUM REMARK 210 CHLORIDE, 50 UM EDTA, 100 % D2O, REMARK 210 0.2 % SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 11ECHO NOESY; 2D WATERGATE REMARK 210 NOESY; 2D 1H-13C S3CT HSQC; 2D REMARK 210 1H-13C HSQC; 2D 15N CPMG NOESY; REMARK 210 2D TOCSY; 2D 15N HMQC; 2D NOESY; REMARK 210 2D JNN-HNN COSY; 2D HCCH COSY; REMARK 210 3D HCCH-TOCSY; 2D 13C FILTERED/ REMARK 210 EDITED NOESYS; 3D 13C HSQC NOESY; REMARK 210 2D 1H-15N HSQC 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 : MOLMOL 2K.2, SPARKY, XWINNMR 3.5 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 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 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 HO2' G A 93 O5' G A 94 1.39 REMARK 500 O2' A A 111 H5' C A 112 1.47 REMARK 500 HO2' A A 175 O5' A A 176 1.50 REMARK 500 HO2' G A 94 O4' G A 95 1.55 REMARK 500 H5'' U A 105 OP1 C A 106 1.59 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 93 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 93 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 94 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 94 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 95 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 95 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 98 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 98 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 U A 99 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 107 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 107 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 110 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 110 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 111 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 117 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 118 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 118 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 167 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 168 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 169 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 171 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 171 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 172 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 173 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 174 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 175 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 176 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 178 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 178 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 181 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 182 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 182 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 184 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 93 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 93 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 94 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 94 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 95 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 95 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 98 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 98 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 U A 99 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 107 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 107 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 110 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 110 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 111 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 117 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 118 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 118 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 656 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YMO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE MINIMAL HUMAN TELOMERASE RNA PSEUDOKNOT REMARK 900 RELATED ID: 1NA2 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF P2B HAIRPIN FROM HUMAN TELOMERASE RNA REMARK 900 RELATED ID: 2K96 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE RDC-REFINED P2B-P3 PSEUDOKNOT FROM HUMAN REMARK 900 TELOMERASE RNA (DELTA U177) DBREF 2K95 A 93 184 PDB 2K95 2K95 93 184 SEQRES 1 A 48 G G G C U G U U U U U C U SEQRES 2 A 48 C G C U G A C U U U C A G SEQRES 3 A 48 C C C C A A A C A A A A A SEQRES 4 A 48 A U 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