HEADER RNA 08-DEC-09 2KR8 OBSLTE 09-JUN-10 2KR8 2XEB TITLE NMR STRUCTURE OF THE PROTEIN-UNBOUND SPLICEOSOMAL U4 SNRNA 5' STEM TITLE 2 LOOP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*U COMPND 3 P*U)-3'; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: U4 5'-SL STRAND A, RESIDUES 19-37; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3'; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: U4 5'-SL STRAND B, RESIDUES 40-53; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: RNA SYNTHESIZED WITH IN VITRO TRANSCRIPTION USING T7 SOURCE 7 RNA POLYMERASE (OBTAINED WITH E.COLI); SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 OTHER_DETAILS: RNA SYNTHESIZED WITH IN VITRO TRANSCRIPTION USING T7 SOURCE 14 RNA POLYMERASE (OBTAINED WITH E.COLI) KEYWDS U4 SNRNA, RNA STRUCTURE, U4/U6 DI-SNRNP, PRE-MRNA SPLICING, KINK-TURN KEYWDS 2 DOMAIN, RNP-BINDING DOMAIN, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.FALB,I.AMATA,B.SIMON,T.CARLOMAGNO REVDAT 3 09-JUN-10 2KR8 1 OBSLTE REVDAT 2 02-JUN-10 2KR8 1 JRNL REVDAT 1 05-MAY-10 2KR8 0 JRNL AUTH M.FALB,I.AMATA,F.GABEL,B.SIMON,T.CARLOMAGNO JRNL TITL STRUCTURE OF THE K-TURN U4 RNA: A COMBINED NMR AND SANS JRNL TITL 2 STUDY JRNL REF NUCLEIC ACIDS RES. 2010 JRNL REFN ESSN 1362-4962 JRNL PMID 20466811 JRNL DOI 10.1093/NAR/GKQ380 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, CNS 1.1 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KR8 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-09. REMARK 100 THE RCSB ID CODE IS RCSB101473. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 7.6; 7.6 REMARK 210 IONIC STRENGTH : 120; 120 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3MM [U-100% 13C; U-100% 15N] REMARK 210 RNA (5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP* REMARK 210 UP*U)-3')-1, 0.45MM RNA (5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP* REMARK 210 AP*UP*C)-3')-2, 20MM HEPES-3, 120MM NACL-4, 90% H2O/10% D2O, 100% REMARK 210 D2O; 0.3MM [U-100% 13C; U-100% 15N] RNA (5'-R(P*GP*CP*CP*GP*AP* REMARK 210 GP*GP*CP*GP*CP*GP*AP*UP*C)-3')-5, 0.45MM RNA (5'-R(P*GP*AP*UP*CP* REMARK 210 GP*UP*AP*GP*CP*CP*AP*AP*UP*GP*AP*GP*GP*UP*U)-3')-6, 20MM HEPES-7, REMARK 210 120MM NACL-8, 90% H2O/10% D2O, 100% D2O; 0.3MM [U-100% 13C; U- REMARK 210 100% 15N] RNA (5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP* REMARK 210 AP*GP*GP*UP*U)-3')-9, 0.3MM [U-100% 13C; U-100% 15N] RNA (5'-R(P* REMARK 210 GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3')-10, 20MM HEPES-11, REMARK 210 120MM NACL-12, 90% H2O/10% D2O, 100% D2O; 0.3MM [U-10% 13C; U- REMARK 210 100% 15N] RNA (5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP* REMARK 210 AP*GP*GP*UP*U)-3')-13, 0.45MM RNA (5'-R(P*GP*CP*CP*GP*AP*GP*GP* REMARK 210 CP*GP*CP*GP*AP*UP*C)-3')-14, 20MM HEPES-15, 120MM NACL-16, 10- REMARK 210 15MG/ML BACTERIOPHAGES-17, 100% D2O; 0.3MM [U-100% 13C; U-100% REMARK 210 15N] RNA (5'-R(P*GP*CP*CP*GP*AP*GP*GP*CP*GP*CP*GP*AP*UP*C)-3')- REMARK 210 18, 0.45MM RNA (5'-R(P*GP*AP*UP*CP*GP*UP*AP*GP*CP*CP*AP*AP*UP*GP* REMARK 210 AP*GP*GP*UP*U)-3')-19, 20MM HEPES-20, 120MM NACL-21, 10-15MG/ML REMARK 210 BACTERIOPHAGES-22, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 2D 1H-1H NOESY; 3D-13C-EDITED,13C REMARK 210 -FILTERED NOESY; 2D-13C-EDITED, REMARK 210 12C-FILTERED NOESY; 3D-COSY- REMARK 210 TOCSY; 3D-HCN; 3D-TROSY RELAYED REMARK 210 HCCH-COSY; 2D-HNN-COSY; 3D-ECOSY; REMARK 210 3D-HCP REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA/CNS 1.2/1.1, FELIX REMARK 210 METHOD USED : RDC REFINEMENT, WATER REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1568 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6782 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 H62 A A 33 H21 G B 43 1.30 REMARK 500 H1' G A 32 H62 A B 44 1.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 A A 20 C2' A A 20 C1' -0.049 REMARK 500 2 G A 35 C2' G A 35 C1' -0.057 REMARK 500 3 G A 19 C2' G A 19 C1' -0.049 REMARK 500 4 G A 35 C2' G A 35 C1' -0.057 REMARK 500 7 A A 20 C2' A A 20 C1' -0.049 REMARK 500 7 G A 35 C2' G A 35 C1' -0.057 REMARK 500 8 A A 20 C2' A A 20 C1' -0.050 REMARK 500 9 G A 35 C2' G A 35 C1' -0.055 REMARK 500 10 G A 35 C2' G A 35 C1' -0.057 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 2 G A 35 0.05 SIDE CHAIN REMARK 500 4 G A 35 0.05 SIDE CHAIN REMARK 500 7 G A 35 0.05 SIDE CHAIN REMARK 500 9 G A 35 0.05 SIDE CHAIN REMARK 500 10 G A 35 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OZB RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE U4 SNRNA 5' STEM LOOP BOUND TO 15.5K REMARK 900 AND HPRP31 REMARK 900 RELATED ID: 1E7K RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE SPLICEOSOMAL 15.5K BOUND TO U4 SNRNA REMARK 900 FRAGMENT DBREF 2KR8 A 19 37 GB 36174 V00592 19 37 DBREF 2KR8 B 40 53 GB 36174 V00592 40 53 SEQADV 2KR8 G A 19 GB 36174 U 19 ENGINEERED SEQADV 2KR8 G B 40 GB 36174 U 40 ENGINEERED SEQADV 2KR8 C B 53 GB 36174 U 53 ENGINEERED SEQRES 1 A 19 G A U C G U A G C C A A U SEQRES 2 A 19 G A G G U U SEQRES 1 B 14 G C C G A G G C G C G A U SEQRES 2 B 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