HEADER RNA 23-FEB-00 1EI2 TITLE STRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN THE TAU TITLE 2 EXON 10 SPLICING REGULATORY ELEMENT BY AMINOGLYCOSIDE ANTIBIOTICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAU EXON 10 SRE RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TAU EXON 10 SPLICING REGULATORY ELEMENT; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPLEXED WITH ANTIBIOTIC NEOMYCIN SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS RNA, TAU, FRONTOTEMPORAL DEMENTIA FTDP-17, INTRONIC MUTATIONS, KEYWDS 2 AMINOGLYCOSIDE, RNA MAJOR GROOVE RECOGNITION EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR L.VARANI,M.G.SPILLANTINI,M.GOEDERT,G.VARANI REVDAT 4 01-FEB-17 1EI2 1 AUTHOR VERSN REVDAT 3 24-FEB-09 1EI2 1 VERSN REVDAT 2 01-APR-03 1EI2 1 JRNL REVDAT 1 06-MAR-00 1EI2 0 JRNL AUTH L.VARANI,M.G.SPILLANTINI,M.GOEDERT,G.VARANI JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF THE RNA MAJOR GROOVE IN JRNL TITL 2 THE TAU EXON 10 SPLICING REGULATORY ELEMENT BY JRNL TITL 3 AMINOGLYCOSIDE ANTIBIOTICS. JRNL REF NUCLEIC ACIDS RES. V. 28 710 2000 JRNL REFN ISSN 0305-1048 JRNL PMID 10637322 JRNL DOI 10.1093/NAR/28.3.710 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS CALCULATED STARTING REMARK 3 FROM RANDOM COORDINATES. NO MANUAL OR AUTOMATIC DOCKING STEP WAS REMARK 3 USED AT ANY STAGE OF THE CALCULATION. REMARK 4 REMARK 4 1EI2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-00. REMARK 100 THE RCSB ID CODE IS RCSB010594. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 10MM POTASSIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM TAU EXON 10 SRE RNA U-13C, REMARK 210 15N; 10MM PHOSPHATE BUFFER, PH 6; REMARK 210 1MM NEOMYCIN UNLABELLED REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C-SEPARATED_ REMARK 210 NOESY; 2D TOCSY; 2D 13C HSQC; 2D REMARK 210 15N HSQC; HCCP, HETEROTOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.8, FELIX 97.0, XWINNMR REMARK 210 2.0 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: 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 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 2 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 321 ANGLE DEVIATIONS. 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 NMY A 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QC8 RELATED DB: PDB REMARK 900 1QC8 CONTAINS THE STRUCTURE OF THE FREE RNA DBREF 1EI2 A 1 25 PDB 1EI2 1EI2 1 25 SEQRES 1 A 25 G G C A G U G U G A G U A SEQRES 2 A 25 C C U U C A C A C G U C HET NMY A 26 88 HETNAM NMY NEOMYCIN HETSYN NMY MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN FORMUL 2 NMY C23 H46 N6 O13 SITE 1 AC1 9 G A 5 U A 6 G A 7 U A 8 SITE 2 AC1 9 C A 14 U A 17 C A 18 A A 19 SITE 3 AC1 9 C A 20 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