HEADER DE-NOVO PROTEIN/RNA 19-MAR-01 1I9F TITLE STRUCTURAL CHARACTERIZATION OF THE COMPLEX OF THE REV RESPONSE ELEMENT TITLE 2 RNA WITH A SELECTED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REV RESPONSE ELEMENT RNA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RRE, HIV-1 RRE RNA; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: 34-MER RNA; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RSG-1.2 PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: 19-MER PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE NATURALLY OCCURS IN HUMAN IMMUNODEFICIENCY SOURCE 4 VIRUS TYPE 1, STRAIN DH5A; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS PEPTIDE-RNA COMPLEX, RNA RECOGNITION, SELECTED PEPTIDE, SOLUTION KEYWDS 2 STRUCTURE, DE-NOVO PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR Q.ZHANG,K.HARADA,H.S.CHO,A.FRANKEL,D.E.WEMMER REVDAT 5 22-MAY-24 1I9F 1 REMARK REVDAT 4 23-FEB-22 1I9F 1 REMARK REVDAT 3 24-FEB-09 1I9F 1 VERSN REVDAT 2 01-APR-03 1I9F 1 JRNL REVDAT 1 25-MAY-01 1I9F 0 JRNL AUTH Q.ZHANG,K.HARADA,H.S.CHO,A.D.FRANKEL,D.E.WEMMER JRNL TITL STRUCTURAL CHARACTERIZATION OF THE COMPLEX OF THE REV JRNL TITL 2 RESPONSE ELEMENT RNA WITH A SELECTED PEPTIDE. JRNL REF CHEM.BIOL. V. 8 511 2001 JRNL REFN ISSN 1074-5521 JRNL PMID 11358697 JRNL DOI 10.1016/S1074-5521(01)00027-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I9F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-01. REMARK 100 THE DEPOSITION ID IS D_1000013070. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.6 MM RNA/PEPTIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; DQF-COSY; HNCA-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, FELIX REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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: DIMERIC 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 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 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 2 C5' - C4' - O4' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 7 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 9 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 15 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 19 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 C A 20 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 20 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 24 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 25 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 C A 33 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 34 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 ARG B 202 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 C A 9 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 G A 10 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 G A 15 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 19 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 2 C A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C A 20 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 23 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 G A 31 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 C A 33 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 C A 4 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 3 U A 5 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 G A 8 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 C A 9 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES REMARK 500 3 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 C A 11 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 3 C A 11 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 A A 12 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 G A 15 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 G A 15 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 C A 16 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 19 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G A 22 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 A A 23 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 3 A A 23 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 3 C A 24 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 31 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 G A 32 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 115 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 ARG B 202 76.71 46.15 REMARK 500 1 SER B 204 -121.49 -122.75 REMARK 500 1 PRO B 206 33.55 -77.73 REMARK 500 1 ALA B 216 14.23 -67.15 REMARK 500 3 ARG B 202 79.45 -157.82 REMARK 500 3 SER B 204 36.95 -72.50 REMARK 500 4 ARG B 202 88.26 30.83 REMARK 500 4 SER B 204 60.65 24.85 REMARK 500 5 ARG B 202 63.88 24.72 REMARK 500 5 ALA B 209 12.23 59.04 REMARK 500 5 ALA B 218 50.14 -147.47 REMARK 500 6 ARG B 202 74.88 -156.01 REMARK 500 6 SER B 204 -95.93 -121.13 REMARK 500 6 ARG B 205 70.06 51.35 REMARK 500 6 SER B 207 170.30 -55.35 REMARK 500 7 ARG B 202 104.31 -174.08 REMARK 500 7 SER B 204 53.41 34.64 REMARK 500 7 ALA B 218 81.78 -161.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 206 SER B 207 5 -121.88 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 1 0.07 SIDE CHAIN REMARK 500 1 G A 2 0.06 SIDE CHAIN REMARK 500 1 U A 5 0.11 SIDE CHAIN REMARK 500 1 G A 6 0.11 SIDE CHAIN REMARK 500 1 G A 10 0.10 SIDE CHAIN REMARK 500 1 A A 12 0.06 SIDE CHAIN REMARK 500 1 C A 14 0.08 SIDE CHAIN REMARK 500 1 G A 15 0.09 SIDE CHAIN REMARK 500 1 C A 16 0.07 SIDE CHAIN REMARK 500 1 G A 19 0.23 SIDE CHAIN REMARK 500 1 C A 24 0.13 SIDE CHAIN REMARK 500 1 C A 33 0.09 SIDE CHAIN REMARK 500 1 ARG B 201 0.10 SIDE CHAIN REMARK 500 1 ARG B 212 0.09 SIDE CHAIN REMARK 500 2 G A 2 0.05 SIDE CHAIN REMARK 500 2 G A 6 0.08 SIDE CHAIN REMARK 500 2 G A 7 0.07 SIDE CHAIN REMARK 500 2 G A 8 0.07 SIDE CHAIN REMARK 500 2 G A 10 0.05 SIDE CHAIN REMARK 500 2 C A 14 0.07 SIDE CHAIN REMARK 500 2 G A 15 0.09 SIDE CHAIN REMARK 500 2 C A 16 0.08 SIDE CHAIN REMARK 500 2 G A 19 0.17 SIDE CHAIN REMARK 500 2 G A 22 0.07 SIDE CHAIN REMARK 500 2 A A 23 0.07 SIDE CHAIN REMARK 500 2 G A 26 0.10 SIDE CHAIN REMARK 500 2 A A 30 0.07 SIDE CHAIN REMARK 500 2 C A 33 0.10 SIDE CHAIN REMARK 500 2 ARG B 212 0.09 SIDE CHAIN REMARK 500 3 G A 1 0.09 SIDE CHAIN REMARK 500 3 G A 2 0.06 SIDE CHAIN REMARK 500 3 U A 3 0.12 SIDE CHAIN REMARK 500 3 U A 5 0.09 SIDE CHAIN REMARK 500 3 G A 8 0.07 SIDE CHAIN REMARK 500 3 C A 9 0.06 SIDE CHAIN REMARK 500 3 C A 11 0.08 SIDE CHAIN REMARK 500 3 A A 12 0.14 SIDE CHAIN REMARK 500 3 G A 13 0.08 SIDE CHAIN REMARK 500 3 C A 14 0.06 SIDE CHAIN REMARK 500 3 G A 15 0.10 SIDE CHAIN REMARK 500 3 C A 16 0.08 SIDE CHAIN REMARK 500 3 G A 19 0.12 SIDE CHAIN REMARK 500 3 C A 20 0.07 SIDE CHAIN REMARK 500 3 G A 22 0.07 SIDE CHAIN REMARK 500 3 C A 24 0.11 SIDE CHAIN REMARK 500 3 G A 25 0.13 SIDE CHAIN REMARK 500 3 A A 30 0.05 SIDE CHAIN REMARK 500 3 G A 32 0.07 SIDE CHAIN REMARK 500 4 G A 1 0.08 SIDE CHAIN REMARK 500 4 G A 2 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 110 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1I9F A 1 34 PDB 1I9F 1I9F 1 34 DBREF 1I9F B 201 219 PDB 1I9F 1I9F 201 219 SEQRES 1 A 34 G G U C U G G G C G C A G SEQRES 2 A 34 C G C A A G C U G A C G G SEQRES 3 A 34 U A C A G G C C SEQRES 1 B 19 ARG ARG GLY SER ARG PRO SER GLY ALA GLU ARG ARG ARG SEQRES 2 B 19 ARG ARG ALA ALA ALA ALA HELIX 1 1 SER B 207 ALA B 219 1 13 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