HEADER RNA 11-FEB-11 2Y95 TITLE SOLUTION STRUCTURE OF AUCG TETRALOOP HAIRPIN FOUND IN HUMAN XIST RNA TITLE 2 A-REPEATS ESSENTIAL FOR X-INACTIVATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*GP*CP*AP*UP*CP*GP*GP*CP*GP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HAIRPIN 1, RESIDUES 609-622; COMPND 5 SYNONYM: XIST RNA A-REPEAT, HOMO SAPIENS X (INACTIVE)-SPECIFIC COMPND 6 TRANSCRIPT, XIST; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: HAIRPIN 1 FROM THE 6TH HUMAN A-REPEAT CORRESPONDING TO COMPND 10 NUCLEOTIDES 609-622 IN M97168.1 GENBANK ENTRY. THE THIRD G-C BASE- COMPND 11 PAIR IS REPLACED BY C-G TO FACILITATE CHEMICAL SHIFT ASSIGNMENTS AND COMPND 12 THE CLOSING G-U BASE PAIR IS REPLACED BY G-C SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS RNA, X CHROMOSOME INACTIVATION, RNA STEMLOOP EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.M.DUSZCZYK,M.SATTLER REVDAT 5 19-JUN-24 2Y95 1 REMARK REVDAT 4 14-JUN-23 2Y95 1 REMARK REVDAT 3 24-JAN-18 2Y95 1 REMARK REVDAT 2 21-MAR-12 2Y95 1 REMARK DBREF SEQADV REVDAT 1 26-OCT-11 2Y95 0 JRNL AUTH M.M.DUSZCZYK,A.WUTZ,V.RYBIN,M.SATTLER JRNL TITL THE XIST RNA A-REPEAT COMPRISES A NOVEL AUCG TETRALOOP FOLD JRNL TITL 2 AND A PLATFORM FOR MULTIMERIZATION. JRNL REF RNA V. 17 1973 2011 JRNL REFN ISSN 1355-8382 JRNL PMID 21947263 JRNL DOI 10.1261/RNA.2747411 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.M.DUSZCZYK,M.SATTLER REMARK 1 TITL (1)H, (13)C, (15)N AND (31)P CHEMICAL SHIFT ASSIGNMENTS OF A REMARK 1 TITL 2 HUMAN XIST RNA A-REPEAT TETRALOOP HAIRPIN ESSENTIAL FOR REMARK 1 TITL 3 X-CHROMOSOME INACTIVATION. REMARK 1 REF BIOMOL.NMR ASSIGN. V. 6 75 2012 REMARK 1 REFN ISSN 1874-2718 REMARK 1 PMID 21779925 REMARK 1 DOI 10.1007/S12104-011-9328-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : D.A.CASE,T.A.DARDEN,T.E.CHEATHAM,III, REMARK 3 C.L.SIMMERLING,J.WANG,R.E.DUKE,R.LUO, R.C.WALKER, REMARK 3 W.ZHANG,K.M.MERZ,B.P.ROBERTS, B.WANG,S.HAYIK, REMARK 3 A.ROITBERG,G.SEABRA, I.KOLOSSVARY,K.F.WONG, REMARK 3 F.PAESANI,J.VANICEK, X.WU,S.R.BROZELL, REMARK 3 T.STEINBRECHER,H.GOHLKE, Q.CAI,X.YE,J.WANG,M.- REMARK 3 J.HSIEH,G.CUI,D.R.ROE, D.H.MATHEWS,M.G.SEETIN, REMARK 3 C.SAGUI,V.BABIN, A. LUCHKO,S.GUSAROV,A.KOVALENKO, REMARK 3 P.A.KOLLMAN. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 20 ARIA-CALCULATED STRUCTURES WERE REMARK 3 CHOSEN BASED UPON LOW RESTRAINT VIOLATION AND LOW ENERGY FOR REMARK 3 REFINEMENT WITH AMBER REMARK 4 REMARK 4 2Y95 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1290047361. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278.0; 298.0; 298.0; 278.0; REMARK 210 278.0; 298.0; 298.0; 298.0; 298.0 REMARK 210 PH : 6.0; 6.0; 6.0; 6.0; 6.0; 6.0; REMARK 210 6.0; 6.0; 6.0 REMARK 210 IONIC STRENGTH : 100; 100; 100; 100; 100; 100; REMARK 210 100; 100; 100 REMARK 210 PRESSURE : 1.0 ATM; 1.0 ATM; 1.0 ATM; 1.0 REMARK 210 ATM; 1.0 ATM; 1.0 ATM; 1.0 ATM; REMARK 210 1.0 ATM; 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O; 100% D2O; 90% REMARK 210 H2O/10% D2O; 90% H2O/10% D2O; REMARK 210 100% D2O; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY WITH WATERGATE REMARK 210 AND WATERFLIPBACK; 2D 1H-13C REMARK 210 HSQC; 2D 1H-13C HC-TROSY; 2D 1H- REMARK 210 1H TOCSY; 2D 1H-15N HSQC; HNN- REMARK 210 COSY; 2D 1H-13C SELECTIVE HSQC; REMARK 210 3D HCCH-E.COSY; 3D HCCH-TOCSY; REMARK 210 3D HCN; 3D FORWARD DIRECTED HCCH- REMARK 210 E.COSY; HNN- COSY LONG-RANGE; REMARK 210 HNN-COSY WITH ADIABATIC REMARK 210 REFOCUSING; TROSY RELAYED HCCH- REMARK 210 COSY; 2D 1H-13C HMQC; 3D 1H-13C REMARK 210 NOESY-HMQC; 3D HCP; 3D HCP SPIN- REMARK 210 ECHO-DIFF; 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, ARIA 1.2, REMARK 210 AMBER REMARK 210 METHOD USED : ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION, LOW REMARK 210 ENERGY, AGREEMENT WITH CHEMICAL REMARK 210 SHIFTS CALCULATED BY NUCHEMICS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 100 INITIAL STRUCTURES WERE CALCULATED USING ARIA, 20 WERE REMARK 210 SELECTED FOR REFINEMENT WITH AMBER, OF WHICH 10 WERE SELECTED REMARK 210 FOR DEPOSITION BASED ON LOW ENERGY CRITERIA AND AGREEMENT REMARK 210 BETWEEN CALCULATED AND EXPERIMENTAL CHEMICAL SHIFTS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, C 612 TO G REMARK 400 ENGINEERED RESIDUE IN CHAIN A, G 619 TO C REMARK 400 ENGINEERED RESIDUE IN CHAIN A, U 622 TO C 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 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 U A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16714 RELATED DB: BMRB DBREF 2Y95 A 1 14 GB 340393 M97168 609 622 SEQADV 2Y95 G A 4 GB 340393 C 612 ENGINEERED MUTATION SEQADV 2Y95 C A 11 GB 340393 G 619 ENGINEERED MUTATION SEQADV 2Y95 C A 14 GB 340393 U 622 ENGINEERED MUTATION SEQRES 1 A 14 G G C G C A U C G G C G C SEQRES 2 A 14 C 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 TER 453 C A 14 ENDMDL MODEL 2 TER 453 C A 14 ENDMDL MODEL 3 TER 453 C A 14 ENDMDL MODEL 4 TER 453 C A 14 ENDMDL MODEL 5 TER 453 C A 14 ENDMDL MODEL 6 TER 453 C A 14 ENDMDL MODEL 7 TER 453 C A 14 ENDMDL MODEL 8 TER 453 C A 14 ENDMDL MODEL 9 TER 453 C A 14 ENDMDL MODEL 10 TER 453 C A 14 ENDMDL MASTER 138 0 0 0 0 0 0 6 297 1 0 2 END