HEADER RNA 23-AUG-01 1JU7 TITLE NMR SOLUTION STRUCTURE OF THE RNA HAIRPIN BINDING SITE FOR THE HISTONE TITLE 2 STEM-LOOP BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*CP*AP*AP*AP*GP*GP*CP*CP*CP*UP*UP*UP*UP*CP*AP COMPND 3 *GP*GP*GP*CP*CP*AP*CP*CP*CP*A)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HISTONE MRNA 3' STEM LOOP SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY AT THE 3' END OF THE SOURCE 4 REPLICATION-DEPENDENT HISTONE MRNAS OF VERTEBRATES. THIS SEQUENCE SOURCE 5 CORRESPONDS TO THE MOUSE H4-12 GENE. KEYWDS HAIRPIN, TETRALOOP, 3' STACK, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.S.DEJONG,W.F.MARZLUFF,E.P.NIKONOWICZ REVDAT 4 23-FEB-22 1JU7 1 REMARK REVDAT 3 24-FEB-09 1JU7 1 VERSN REVDAT 2 01-APR-03 1JU7 1 JRNL REVDAT 1 20-MAR-02 1JU7 0 JRNL AUTH E.S.DEJONG,W.F.MARZLUFF,E.P.NIKONOWICZ JRNL TITL NMR STRUCTURE AND DYNAMICS OF THE RNA-BINDING SITE FOR THE JRNL TITL 2 HISTONE MRNA STEM-LOOP BINDING PROTEIN. JRNL REF RNA V. 8 83 2002 JRNL REFN ISSN 1355-8382 JRNL PMID 11871662 JRNL DOI 10.1017/S1355838202013869 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 980, X-PLOR 3.851 REMARK 3 AUTHORS : MSI-BIOSYM (FELIX), BRUNGER, A. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CALCULATIONS WERE PERFORMED USING 232 REMARK 3 CONFORMATIONALLY RESTRICTIVE NOE DERIVED DISTANCE CONSTRAINTS REMARK 3 AND 55 BACKBONE AND 15 RIBOSE TORSION ANGLE CONSTRAINTS. BASE REMARK 3 PAIR CONSTRAINTS WERE INTRODUCED FOR SIX BASE PAIRS USING HEAVY REMARK 3 ATOM-HEAVY ATOM CONSTRAINTS. COORDINATES ARE FOR THE HAIRPIN REMARK 3 DOMAIN ONLY. 5' FLANKING (GGCCAAA) AND 3' FLANKING (ACCCA) REMARK 3 COORDINATES ARE NOT INCLUDED WITH THIS DEPOSITION. FEW REMARK 3 CONSTRAINTS WERE OBTAINED FOR THESE VERY DYNAMIC REGIONS AND REMARK 3 ALTHOUGH THEY WERE INCLUDED AS PART OF THE STRUCTURE CALCULATION, REMARK 3 THEIR CONFORMATIONS APPEAR TO BE RANDOMLY DISTRIBUTED. REMARK 4 REMARK 4 1JU7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014190. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301; 280; 301 REMARK 210 PH : 6.8; 6.8; 6.8 REMARK 210 IONIC STRENGTH : 100 MM; 100 MM; 100 MM REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.3 MM U-13C; 20 MM KPI, 20 MM REMARK 210 KCL, 0.02 MM EDTA, PH 6.8; 2.5 REMARK 210 MM U-15N; 20 MM KPI, 20 MM KCL, REMARK 210 0.02 MM EDTA, PH 6.8; 2.0 MM U- REMARK 210 13C,C5-2H; 20 MM KPI, 20 MM KCL, REMARK 210 0.02 MM EDTA, PH 6.8; 2.8 MM REMARK 210 UNLABELED 20 MM KPI, 20 MM KCL, REMARK 210 0.02 MM EDTA, PH 6.8 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; 3D_13C-SEPARATED_NOESY; REMARK 210 3D_15N-SEPARATED_NOESY; DQF-COSY; REMARK 210 HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS, STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING A VARIETY OF 2D AND 3D REMARK 210 HOMO- AND HETERO-NUCLEAR NMR METHODS. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 G A -6 REMARK 465 G A -5 REMARK 465 C A -4 REMARK 465 C A -3 REMARK 465 A A -2 REMARK 465 A A -1 REMARK 465 A A 0 REMARK 465 A A 17 REMARK 465 C A 18 REMARK 465 C A 19 REMARK 465 C A 20 REMARK 465 A A 21 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 G A 1 P OP1 OP2 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 HO2' C A 5 O5' U A 6 1.41 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 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. = -2.8 DEGREES REMARK 500 1 C A 10 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 1 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 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. = -2.9 DEGREES REMARK 500 2 U A 7 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 U A 7 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 3 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 11 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 3 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 2 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 4 C A 10 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 4 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 4 G A 13 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 13 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 4 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 5 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 120 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1JU7 A -6 21 GB 51308 X13235 573 600 SEQADV 1JU7 G A -6 GB 51308 A 573 SEE REMARK 999 SEQADV 1JU7 G A -5 GB 51308 A 574 SEE REMARK 999 SEQADV 1JU7 C A -3 GB 51308 A 576 SEE REMARK 999 SEQRES 1 A 28 G G C C A A A G G C C C U SEQRES 2 A 28 U U U C A G G G C C A C C SEQRES 3 A 28 C A CRYST1 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