2KM3 - Header Asymmetric Unit

HEADER DNA 17-JUL-09 2KM3

TITLE STRUCTURE OF AN INTRAMOLECULAR G-QUADRUPLEX CONTAINING A TITLE 2 G.C.G.C TETRAD FORMED BY HUMAN TELOMERIC VARIANT CTAGGG TITLE 3 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 COMPND 4 *GP*GP*G)-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 KEYWDS 2 TELOMERE INSTABILITY, DNA

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR K.W.LIM,P.ALBERTI,A.GUEDIN,L.LACROIX,J.F.RIOU,N.J.ROYLE, AUTHOR 2 J.L.MERGNY,A.T.PHAN

REVDAT 1 03-NOV-09 2KM3 0

JRNL AUTH K.W.LIM,P.ALBERTI,A.GUEDIN,L.LACROIX,J.F.RIOU, JRNL AUTH 2 N.J.ROYLE,J.L.MERGNY,A.T.PHAN JRNL TITL SEQUENCE VARIANT (CTAGGG)N IN THE HUMAN TELOMERE JRNL TITL 2 FAVORS A G-QUADRUPLEX STRUCTURE CONTAINING A JRNL TITL 3 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 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.21 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2KM3 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB101290.

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'-D(*AP*GP* REMARK 210 GP*GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP*GP*GP*CP*TP*AP*GP*GP*G)-3' REMARK 210 )-1, 70MM POTASSIUM CHLORIDE, 20MM POTASSIUM PHOSPHATE, 90% REMARK 210 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- REMARK 210 13C HMBC; 2D 1H-13C JR HMBC; H REMARK 210 -D EXCHANGE; 15N-FILTERED; D- REMARK 210 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 : TOPSPIN, FELIX 2007, X-PLOR_ REMARK 210 NIH 2.21 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY REMARK 210 SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, 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 REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 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 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 HO5' DA A 1 OP1 DG A 2 1.48 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 REMARK 900 PRESENCE OF K REMARK 900 RELATED ID: 2JSK RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K REMARK 900 CATIONS 16BRG FORM 1 REMARK 900 RELATED ID: 2JSL RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K REMARK 900 CATIONS 16BRG FORM 1 REMARK 900 RELATED ID: 2JSM RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K REMARK 900 CATIONS NATURAL FORM 1 REMARK 900 RELATED ID: 2JSQ RELATED DB: PDB REMARK 900 HUMAN TELOMERE DNA SOLUTION STRUCTURE IN THE PRESENCE OF K REMARK 900 CATIONS FORM 2 15BRG REMARK 900 RELATED ID: 2KF7 RELATED DB: PDB REMARK 900 STRUCTURE OF A TWO-G-TETRAD BASKET-TYPE INTRAMOLECULAR G- REMARK 900 QUADRUPLEX FORMED BY HUMAN TELOMERIC REPEATS IN K+ SOLUTION REMARK 900 (7BRG) REMARK 900 RELATED ID: 2KF8 RELATED DB: PDB REMARK 900 STRUCTURE OF A TWO-G-TETRAD BASKET-TYPE INTRAMOLECULAR G- REMARK 900 QUADRUPLEX 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