HEADER MEMBRANE PROTEIN/RNA 24-DEC-13 2RU7 TITLE REFINED STRUCTURE OF RNA APTAMER IN COMPLEX WITH THE PARTIAL BINDING TITLE 2 PEPTIDE OF PRION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA_(5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: P16 PEPTIDE FROM MAJOR PRION PROTEIN; COMPND 7 CHAIN: C, D; COMPND 8 SYNONYM: PRP, MAJOR SCRAPIE-ASSOCIATED FIBRIL PROTEIN 1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 6 ORGANISM_COMMON: BOVINE; SOURCE 7 ORGANISM_TAXID: 9913; SOURCE 8 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS APTAMER, PRION, RNA, ALZHEIMER'S DISEASE, MEMBRANE PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR T.HAYASHI,H.OSHIMA,T.MASHIMA,T.NAGATA,M.KATAHIRA,M.KINOSHITA REVDAT 3 14-JUN-23 2RU7 1 REMARK REVDAT 2 24-AUG-22 2RU7 1 JRNL REMARK REVDAT 1 21-MAY-14 2RU7 0 JRNL AUTH T.HAYASHI,H.OSHIMA,T.MASHIMA,T.NAGATA,M.KATAHIRA,M.KINOSHITA JRNL TITL BINDING OF AN RNA APTAMER AND A PARTIAL PEPTIDE OF A PRION JRNL TITL 2 PROTEIN: CRUCIAL IMPORTANCE OF WATER ENTROPY IN MOLECULAR JRNL TITL 3 RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 42 6861 2014 JRNL REFN ESSN 1362-4962 JRNL PMID 24803670 JRNL DOI 10.1093/NAR/GKU382 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, X-PLOR NIH 2.26, AMBER 12 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, ... REMARK 3 AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000150272. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 303 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 10; 10 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM RNA (5' REMARK 210 -R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-1, 1 MM P16-2, 10 MM REMARK 210 POTASSIUM PHOSPHATE-3, 10 MM POTASSIUM CHLORIDE-4, 0.01 MM DSS-5, REMARK 210 3 MM SODIUM AZIDE-6, 95% H2O/5% D2O; 1 MM RNA (5'-R(*GP*GP*AP* REMARK 210 GP*GP*AP*GP*GP*AP*GP*GP*A)-3')-7, 1 MM P16-8, 10 MM POTASSIUM REMARK 210 PHOSPHATE-9, 10 MM POTASSIUM CHLORIDE-10, 0.01 MM DSS-11, 3 MM REMARK 210 SODIUM AZIDE-12, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-13C HSQC; REMARK 210 JRHMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, SPARKY, TALOS, REMARK 210 X-PLOR NIH 2.26 REMARK 210 METHOD USED : ENERGY MINIMIZATION, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 A A 3 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 A A 6 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 6 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 A A 6 N1 - C6 - N6 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 A A 9 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 9 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 9 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 12 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 G B 13 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G B 14 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 A B 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A B 15 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A B 15 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 A B 18 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A B 18 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 G B 20 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 A B 21 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A B 21 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A B 21 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 G B 22 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 A B 24 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A B 24 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A B 24 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 3 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 A A 6 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 A A 6 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 6 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 G A 7 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 A A 9 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 A A 9 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 A A 9 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 12 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 G B 13 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 G B 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 A B 15 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 A B 15 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A B 15 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 2 G B 17 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 A B 18 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 143 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 TRP C 27 -167.43 -53.13 REMARK 500 1 ASN C 28 39.39 -69.96 REMARK 500 1 PRO C 30 16.28 32.30 REMARK 500 1 LYS C 32 108.99 -52.99 REMARK 500 1 THR C 35 -8.26 54.30 REMARK 500 1 GLN D 38 -145.92 -121.69 REMARK 500 1 TRP D 39 -97.52 -71.54 REMARK 500 1 PRO D 42 39.05 29.64 REMARK 500 1 THR D 47 -49.34 55.54 REMARK 500 2 GLN C 26 -99.40 -128.61 REMARK 500 2 TRP C 27 -108.94 -82.54 REMARK 500 2 PRO C 30 37.23 29.18 REMARK 500 2 LYS C 32 62.98 39.25 REMARK 500 2 THR C 35 19.07 52.59 REMARK 500 2 GLN D 38 -140.64 -129.20 REMARK 500 2 TRP D 39 -95.28 -72.73 REMARK 500 2 PRO D 42 38.47 30.55 REMARK 500 2 THR D 47 -41.70 61.20 REMARK 500 3 TRP C 27 -168.14 -52.78 REMARK 500 3 ASN C 28 45.30 -70.37 REMARK 500 3 PRO C 30 33.61 24.66 REMARK 500 3 SER C 31 52.87 -102.07 REMARK 500 3 THR C 35 -12.92 53.70 REMARK 500 3 GLN D 38 -154.16 -131.77 REMARK 500 3 TRP D 39 -100.82 -62.78 REMARK 500 3 PRO D 42 33.03 29.95 REMARK 500 3 SER D 43 56.42 -94.51 REMARK 500 3 THR D 47 -90.36 45.61 REMARK 500 4 GLN C 26 -155.47 -135.70 REMARK 500 4 TRP C 27 -96.36 -61.25 REMARK 500 4 PRO C 30 35.29 29.84 REMARK 500 4 SER C 31 51.43 -91.06 REMARK 500 4 GLN D 38 -143.16 -111.00 REMARK 500 4 TRP D 39 -104.65 -74.80 REMARK 500 4 PRO D 42 32.53 35.17 REMARK 500 4 THR D 47 79.04 55.68 REMARK 500 5 GLN C 26 -138.94 -132.97 REMARK 500 5 TRP C 27 -93.77 -69.13 REMARK 500 5 PRO C 30 35.71 29.67 REMARK 500 5 SER C 31 49.87 -107.83 REMARK 500 5 LYS C 32 105.68 -56.23 REMARK 500 5 THR C 35 -39.97 53.57 REMARK 500 5 GLN D 38 -158.93 -141.78 REMARK 500 5 TRP D 39 -165.03 -53.29 REMARK 500 5 ASN D 40 39.44 -70.21 REMARK 500 5 PRO D 42 19.55 31.87 REMARK 500 5 LYS D 44 109.73 -52.52 REMARK 500 5 THR D 47 -10.97 53.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 2 0.09 SIDE CHAIN REMARK 500 1 A A 6 0.13 SIDE CHAIN REMARK 500 1 G A 7 0.08 SIDE CHAIN REMARK 500 1 G A 8 0.08 SIDE CHAIN REMARK 500 1 G A 10 0.10 SIDE CHAIN REMARK 500 1 G B 13 0.07 SIDE CHAIN REMARK 500 1 G B 14 0.06 SIDE CHAIN REMARK 500 1 A B 18 0.06 SIDE CHAIN REMARK 500 1 G B 19 0.10 SIDE CHAIN REMARK 500 1 A B 21 0.07 SIDE CHAIN REMARK 500 1 G B 23 0.06 SIDE CHAIN REMARK 500 1 A B 24 0.06 SIDE CHAIN REMARK 500 2 G A 4 0.10 SIDE CHAIN REMARK 500 2 G A 5 0.06 SIDE CHAIN REMARK 500 2 A A 6 0.08 SIDE CHAIN REMARK 500 2 G A 7 0.12 SIDE CHAIN REMARK 500 2 G A 8 0.07 SIDE CHAIN REMARK 500 2 G B 14 0.07 SIDE CHAIN REMARK 500 2 G B 19 0.12 SIDE CHAIN REMARK 500 2 G B 22 0.08 SIDE CHAIN REMARK 500 3 G A 1 0.06 SIDE CHAIN REMARK 500 3 G A 2 0.07 SIDE CHAIN REMARK 500 3 A A 6 0.12 SIDE CHAIN REMARK 500 3 G A 7 0.13 SIDE CHAIN REMARK 500 3 G A 8 0.07 SIDE CHAIN REMARK 500 3 G A 10 0.05 SIDE CHAIN REMARK 500 3 G B 13 0.06 SIDE CHAIN REMARK 500 3 G B 14 0.09 SIDE CHAIN REMARK 500 3 A B 18 0.13 SIDE CHAIN REMARK 500 3 G B 19 0.09 SIDE CHAIN REMARK 500 4 G A 1 0.06 SIDE CHAIN REMARK 500 4 G A 2 0.06 SIDE CHAIN REMARK 500 4 A A 6 0.13 SIDE CHAIN REMARK 500 4 G A 7 0.10 SIDE CHAIN REMARK 500 4 G A 10 0.07 SIDE CHAIN REMARK 500 4 A B 18 0.17 SIDE CHAIN REMARK 500 4 G B 19 0.14 SIDE CHAIN REMARK 500 4 G B 20 0.16 SIDE CHAIN REMARK 500 4 G B 23 0.07 SIDE CHAIN REMARK 500 5 G A 2 0.06 SIDE CHAIN REMARK 500 5 A A 6 0.07 SIDE CHAIN REMARK 500 5 G A 7 0.11 SIDE CHAIN REMARK 500 5 G A 11 0.06 SIDE CHAIN REMARK 500 5 G B 13 0.07 SIDE CHAIN REMARK 500 5 G B 14 0.06 SIDE CHAIN REMARK 500 5 A B 18 0.09 SIDE CHAIN REMARK 500 5 G B 19 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RSK RELATED DB: PDB REMARK 900 RELATED ID: 11489 RELATED DB: BMRB DBREF 2RU7 A 1 12 PDB 2RU7 2RU7 1 12 DBREF 2RU7 B 13 24 PDB 2RU7 2RU7 13 24 DBREF 2RU7 C 25 36 UNP P10279 PRIO_BOVIN 108 119 DBREF 2RU7 D 37 48 UNP P10279 PRIO_BOVIN 108 119 SEQRES 1 A 12 G G A G G A G G A G G A SEQRES 1 B 12 G G A G G A G G A G G A SEQRES 1 C 12 GLY GLN TRP ASN LYS PRO SER LYS PRO LYS THR ASN SEQRES 1 D 12 GLY GLN TRP ASN LYS PRO SER LYS PRO LYS THR ASN 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