HEADER RNA 20-DEC-18 6IZP TITLE SOLUTION STRUCTURE OF THE COMPLEX OF NAPHTHYRIDINE CARBAMATE DIMER AND TITLE 2 AN RNA WITH UGGAA-UGGAA PENTAD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS SCA31, UGGAA REPEAT, SMALL MOLECULE, DRUG, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.NAGANO,T.SHIBATA,K.NAKATANI,G.KAWAI REVDAT 3 14-JUN-23 6IZP 1 REMARK REVDAT 2 20-JAN-21 6IZP 1 JRNL REVDAT 1 25-DEC-19 6IZP 0 JRNL AUTH T.SHIBATA,K.NAGANO,M.UEYAMA,K.NINOMIYA,T.HIROSE,Y.NAGAI, JRNL AUTH 2 K.ISHIKAWA,G.KAWAI,K.NAKATANI JRNL TITL SMALL MOLECULE TARGETING R(UGGAA)N DISRUPTS RNA FOCI AND JRNL TITL 2 ALLEVIATES DISEASE PHENOTYPE IN DROSOPHILA MODEL JRNL REF NAT COMMUN V. 12 2021 JRNL REFN ESSN 2041-1723 JRNL DOI 10.1038/S41467-020-20487-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6IZP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300009855. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 75 UM RNA (29-MER), 150 UM NCD, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.3, SPARKY 3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 H2' A A 3 H6 C A 4 1.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B2R A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B2R A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36227 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE COMPLEX OF NAPHTHYRIDINE CARBAMATE DIMER REMARK 900 AND AN RNA WITH UGGAA-UGGAA PENTAD DBREF 6IZP A 1 29 PDB 6IZP 6IZP 1 29 SEQRES 1 A 29 G U A C U G G A A C A U G SEQRES 2 A 29 U U U C A U G U G G A A G SEQRES 3 A 29 U A C HET B2R A 101 66 HET B2R A 102 66 HETNAM B2R 3-[3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL) HETNAM 2 B2R CARBAMOYLOXY]PROPYLAMINO]PROPYL ~{N}-(7-METHYL-1,8- HETNAM 3 B2R NAPHTHYRIDIN-2-YL)CARBAMATE HETSYN B2R NAPHTHYRIDINE CARBAMATE DIMER FORMUL 2 B2R 2(C26 H29 N7 O4) SITE 1 AC1 7 U A 5 G A 6 G A 7 A A 9 SITE 2 AC1 7 U A 21 G A 22 B2R A 102 SITE 1 AC2 6 U A 5 G A 6 U A 21 G A 22 SITE 2 AC2 6 G A 23 B2R A 101 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