HEADER RNA 27-OCT-17 6BG9 TITLE HYBRID NMR/CRYO-EM STRUCTURE OF THE HIV-1 RNA DIMERIZATION SIGNAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DIMERIZATION SIGNAL; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RNA INERNAL LOOPS, SHEARED GA PAIRS, GU WOBBLE, S-TURN KEYWDS 2 THERMODYNAMICS, RNA EXPDTA ELECTRON MICROSCOPY; SOLUTION NMR NUMMDL 20 AUTHOR M.F.SUMMERS REVDAT 4 01-MAY-24 6BG9 1 REMARK REVDAT 3 01-JAN-20 6BG9 1 REMARK REVDAT 2 21-MAR-18 6BG9 1 JRNL REVDAT 1 21-FEB-18 6BG9 0 JRNL AUTH K.ZHANG,S.C.KEANE,Z.SU,R.N.IROBALIEVA,M.CHEN,V.VAN, JRNL AUTH 2 C.A.SCIANDRA,J.MARCHANT,X.HENG,M.F.SCHMID,D.A.CASE, JRNL AUTH 3 S.J.LUDTKE,M.F.SUMMERS,W.CHIU JRNL TITL STRUCTURE OF THE 30 KDA HIV-1 RNA DIMERIZATION SIGNAL BY A JRNL TITL 2 HYBRID CRYO-EM, NMR, AND MOLECULAR DYNAMICS APPROACH. JRNL REF STRUCTURE V. 26 490 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 29398526 JRNL DOI 10.1016/J.STR.2018.01.001 REMARK 2 REMARK 2 RESOLUTION. 9.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED GB FOR SOLVENT SIMULATION, NOES REMARK 3 AND EM DATA SIMULTANEOUSLY AS RESTRAINTS REMARK 4 REMARK 4 6BG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230770. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM FULLY PROTONATED, 5 MM REMARK 210 NACL, 140 MM KCL, 1 MM MGCL2, REMARK 210 TRIS, 100% D2O; 400 UM REMARK 210 PROTONATED A-H2 AND A,G-RIBOSE REMARK 210 CARBONS A2RGR; ALL OTHER SITES REMARK 210 DEUTERATED A2RGR, 5 MM NACL, 140 REMARK 210 MM KCL, 1 MM MGCL2, 100% D2O; REMARK 210 400 UM PROTONATED A-H2,H8 AND REMARK 210 FULLY PROTONATED G; ALL OTHER REMARK 210 SITES DEUTERATED A28GH, 5 MM REMARK 210 NACL, 140 MM KCL, 1 MM MGCL2, REMARK 210 100% D2O; 400 UM PROTONATED G-H8, REMARK 210 C-H6,RIBOSE; ALL OTHER SITES REMARK 210 DEUTERATED G8C6R, 5 MM NACL, 140 REMARK 210 MM KCL, 1 MM MGCL2, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY (2H-EDITED); ABUNDANCE REMARK 210 13C-1H HMQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFX, NMRVIEW, CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NMR STUDIES CONDUCTED WITH MULTIPLE SAMPLES PREPARED BY REMARK 210 DIFFERENTIAL NUCLEOTIDE-SPECIFIC 2H LABELING. 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 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SUBTOMOGRAM AVERAGING REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HUMAN IMMUNODEFICIENCY VIRUS 1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : UNSPECIFIED REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.20 REMARK 245 SAMPLE DETAILS : RNA PREPARED BY IN VITRO REMARK 245 TRANSCRIPTION USING T7 RNA POLYMERASE REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : JEOL 2200FS REMARK 245 DETECTOR TYPE : DIRECT ELECTRON DE-12 (4K X REMARK 245 3K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 7500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 25000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 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 A A 4 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 4 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 C A 8 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 G A 12 N3 - C2 - N2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 13 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 C A 17 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 20 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 20 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 21 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 21 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 21 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 G A 22 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C A 23 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 27 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 A A 28 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 28 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 28 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 C A 29 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 C A 32 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 A A 33 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 33 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 33 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 A A 34 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 34 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 34 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 A A 36 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 38 N1 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 C A 39 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 41 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 41 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 41 N1 - C6 - N6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 G A 44 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C A 46 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 47 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A B 51 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 A B 51 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A B 51 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 G B 53 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 A B 54 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A B 54 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 C B 55 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C B 57 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1705 ANGLE DEVIATIONS. 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 5 0.14 SIDE CHAIN REMARK 500 1 G A 11 0.07 SIDE CHAIN REMARK 500 1 G A 12 0.07 SIDE CHAIN REMARK 500 1 U A 14 0.08 SIDE CHAIN REMARK 500 1 G A 19 0.08 SIDE CHAIN REMARK 500 1 G A 24 0.09 SIDE CHAIN REMARK 500 1 G A 26 0.11 SIDE CHAIN REMARK 500 1 G A 31 0.07 SIDE CHAIN REMARK 500 1 A A 33 0.10 SIDE CHAIN REMARK 500 1 A A 34 0.06 SIDE CHAIN REMARK 500 1 G A 35 0.07 SIDE CHAIN REMARK 500 1 G A 37 0.06 SIDE CHAIN REMARK 500 1 G A 38 0.06 SIDE CHAIN REMARK 500 1 G A 40 0.10 SIDE CHAIN REMARK 500 1 A A 41 0.08 SIDE CHAIN REMARK 500 1 G A 44 0.10 SIDE CHAIN REMARK 500 1 G B 52 0.12 SIDE CHAIN REMARK 500 1 G B 59 0.07 SIDE CHAIN REMARK 500 1 U B 61 0.08 SIDE CHAIN REMARK 500 1 G B 63 0.08 SIDE CHAIN REMARK 500 1 G B 66 0.09 SIDE CHAIN REMARK 500 1 G B 71 0.08 SIDE CHAIN REMARK 500 1 C B 72 0.06 SIDE CHAIN REMARK 500 1 G B 73 0.09 SIDE CHAIN REMARK 500 1 A B 80 0.08 SIDE CHAIN REMARK 500 1 A B 81 0.07 SIDE CHAIN REMARK 500 1 G B 85 0.06 SIDE CHAIN REMARK 500 1 G B 87 0.08 SIDE CHAIN REMARK 500 1 A B 88 0.09 SIDE CHAIN REMARK 500 1 G B 91 0.10 SIDE CHAIN REMARK 500 2 G A 5 0.14 SIDE CHAIN REMARK 500 2 G A 12 0.07 SIDE CHAIN REMARK 500 2 U A 14 0.07 SIDE CHAIN REMARK 500 2 G A 19 0.08 SIDE CHAIN REMARK 500 2 G A 24 0.10 SIDE CHAIN REMARK 500 2 G A 26 0.09 SIDE CHAIN REMARK 500 2 A A 33 0.08 SIDE CHAIN REMARK 500 2 A A 34 0.07 SIDE CHAIN REMARK 500 2 G A 38 0.06 SIDE CHAIN REMARK 500 2 G A 40 0.08 SIDE CHAIN REMARK 500 2 A A 41 0.08 SIDE CHAIN REMARK 500 2 G A 44 0.10 SIDE CHAIN REMARK 500 2 G B 52 0.13 SIDE CHAIN REMARK 500 2 G B 58 0.07 SIDE CHAIN REMARK 500 2 G B 59 0.07 SIDE CHAIN REMARK 500 2 U B 61 0.07 SIDE CHAIN REMARK 500 2 G B 66 0.08 SIDE CHAIN REMARK 500 2 G B 71 0.09 SIDE CHAIN REMARK 500 2 G B 73 0.10 SIDE CHAIN REMARK 500 2 A B 80 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 582 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-7080 RELATED DB: EMDB REMARK 900 RELATED ID: 27289 RELATED DB: BMRB DBREF 6BG9 A 1 47 PDB 6BG9 6BG9 1 47 DBREF 6BG9 B 48 94 PDB 6BG9 6BG9 48 94 SEQRES 1 A 47 G G C A G G A C U C G G C SEQRES 2 A 47 U U G C U G A A G C G C G SEQRES 3 A 47 C A C G G C A A G A G G C SEQRES 4 A 47 G A G G G G C C SEQRES 1 B 47 G G C A G G A C U C G G C SEQRES 2 B 47 U U G C U G A A G C G C G SEQRES 3 B 47 C A C G G C A A G A G G C SEQRES 4 B 47 G A G G G G C C CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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