HEADER DNA 17-JUL-09 2KM3 TITLE STRUCTURE OF AN INTRAMOLECULAR G-QUADRUPLEX CONTAINING A G.C.G.C TITLE 2 TETRAD FORMED BY HUMAN TELOMERIC VARIANT CTAGGG REPEATS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*GP*GP*GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP*GP*G)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS KEYWDS ANTICANCER TARGETS, CTAGGG REPEAT, G-QUADRUPLEX, HUMAN TELOMERE KEYWDS 2 INSTABILITY, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.W.LIM,P.ALBERTI,A.GUEDIN,L.LACROIX,J.F.RIOU,N.J.ROYLE,J.L.MERGNY, AUTHOR 2 A.T.PHAN REVDAT 2 01-MAY-24 2KM3 1 REMARK REVDAT 1 03-NOV-09 2KM3 0 JRNL AUTH K.W.LIM,P.ALBERTI,A.GUEDIN,L.LACROIX,J.F.RIOU,N.J.ROYLE, JRNL AUTH 2 J.L.MERGNY,A.T.PHAN JRNL TITL SEQUENCE VARIANT (CTAGGG)N IN THE HUMAN TELOMERE FAVORS A JRNL TITL 2 G-QUADRUPLEX STRUCTURE CONTAINING A G.C.G.C TETRAD JRNL REF NUCLEIC ACIDS RES. V. 37 6239 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19692585 JRNL DOI 10.1093/NAR/GKP630 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, X-PLOR NIH 2.21 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA, CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101290. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 90MM K+ REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-2.0MM DNA (5' REMARK 210 -D(*AP*GP*GP*GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP* REMARK 210 GP*G)-3')-1, 70MM POTASSIUM CHLORIDE, 20MM POTASSIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O; 0.5-2.0MM DNA (5'-D(*AP*GP*GP*GP*CP*TP*AP*GP*GP* REMARK 210 GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP*GP*G)-3')-2, 70MM POTASSIUM REMARK 210 CHLORIDE, 20MM POTASSIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H JR REMARK 210 NOESY; 2D 1H-1H COSY; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-13C HSQC; 2D 1H-13C REMARK 210 HMBC; 2D 1H-13C JR HMBC; H-D REMARK 210 EXCHANGE; 15N-FILTERED; D-LABELED REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2007, X-PLOR NIH 2.21 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 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 DT A 18 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 18 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DT A 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 7 DT A 18 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 8 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 143D RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF NA REMARK 900 RELATED ID: 1K8P RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA CRYSTAL STRUCTURE IN THE PRESENCE OF K REMARK 900 RELATED ID: 2AQY RELATED DB: PDB REMARK 900 3 REPEATS OF HUMAN TELOMERE DNA SOLUTION STRUCTURE REMARK 900 RELATED ID: 2GKU RELATED DB: PDB REMARK 900 END-MODIFIED HUMAN TELOMERE DNA CRYSTAL STRUCTURE IN THE PRESENCE REMARK 900 OF K REMARK 900 RELATED ID: 2JSK RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K CATIONS REMARK 900 16BRG FORM 1 REMARK 900 RELATED ID: 2JSL RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K CATIONS REMARK 900 16BRG FORM 1 REMARK 900 RELATED ID: 2JSM RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K CATIONS REMARK 900 NATURAL FORM 1 REMARK 900 RELATED ID: 2JSQ RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K CATIONS REMARK 900 FORM 2 15BRG REMARK 900 RELATED ID: 2KF7 RELATED DB: PDB REMARK 900 STRUCTURE OF A TWO-G-TETRAD BASKET-TYPE INTRAMOLECULAR G-QUADRUPLEX REMARK 900 FORMED BY HUMAN TELOMERIC REPEATS IN K+ SOLUTION (7BRG) REMARK 900 RELATED ID: 2KF8 RELATED DB: PDB REMARK 900 STRUCTURE OF A TWO-G-TETRAD BASKET-TYPE INTRAMOLECULAR G-QUADRUPLEX REMARK 900 FORMED BY HUMAN TELOMERIC REPEATS IN K+ SOLUTION DBREF 2KM3 A 1 22 PDB 2KM3 2KM3 1 22 SEQRES 1 A 22 DA DG DG DG DC DT DA DG DG DG DC DT DA SEQRES 2 A 22 DG DG DG DC DT DA DG DG DG 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