HEADER RNA 19-OCT-23 8UO6 TITLE HIV-1 REV RESPONSE ELEMENT (RRE) STEM-LOOP II (SLII) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 REV RESPONSE ELEMENT STEM-LOOP II WITH TRNA SCAFFOLD; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 52_53INSG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIV WHOLE-GENOME VECTOR AA1305#18; SOURCE 3 ORGANISM_TAXID: 672471; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NON-CODING RNA, HIV, NUCLEAR EXPORT, RRE, VIRAL RNA, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.TIPO,K.GOTTIPATI,K.CHOI REVDAT 1 05-JUN-24 8UO6 0 JRNL AUTH J.TIPO,K.GOTTIPATI,M.SLATON,G.GONZALEZ-GUTIERREZ,K.H.CHOI JRNL TITL STRUCTURE OF HIV-1 RRE STEM-LOOP II IDENTIFIES TWO JRNL TITL 2 CONFORMATIONAL STATES OF THE HIGH-AFFINITY REV BINDING SITE. JRNL REF NAT COMMUN V. 15 4198 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38760344 JRNL DOI 10.1038/S41467-024-48162-Y REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 61.4 REMARK 3 NUMBER OF REFLECTIONS : 12666 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 605 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 57.1500 - 4.5200 0.99 4929 240 0.1988 0.2169 REMARK 3 2 4.5200 - 3.5900 0.91 4446 235 0.2757 0.3002 REMARK 3 3 3.5900 - 3.1300 0.44 2135 100 0.2703 0.3161 REMARK 3 4 3.1300 - 2.8500 0.11 551 30 0.3367 0.4228 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.333 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 6420 REMARK 3 ANGLE : 0.756 10014 REMARK 3 CHIRALITY : 0.038 1340 REMARK 3 PLANARITY : 0.005 268 REMARK 3 DIHEDRAL : 19.410 3210 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.9755 11.1175 21.6318 REMARK 3 T TENSOR REMARK 3 T11: 0.5805 T22: 0.3524 REMARK 3 T33: 1.0072 T12: 0.3243 REMARK 3 T13: 0.0863 T23: -0.2051 REMARK 3 L TENSOR REMARK 3 L11: 1.7934 L22: 2.0002 REMARK 3 L33: 0.6807 L12: -0.7573 REMARK 3 L13: 0.2018 L23: -0.3029 REMARK 3 S TENSOR REMARK 3 S11: -0.2050 S12: -0.6182 S13: -0.2211 REMARK 3 S21: 1.0274 S22: 0.1694 S23: 0.4643 REMARK 3 S31: -0.1098 S32: -0.2472 S33: -0.0210 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3778 51.4325 33.6669 REMARK 3 T TENSOR REMARK 3 T11: 0.8500 T22: 1.2406 REMARK 3 T33: 0.4966 T12: 0.3981 REMARK 3 T13: -0.0885 T23: 0.0329 REMARK 3 L TENSOR REMARK 3 L11: 0.6441 L22: 3.3715 REMARK 3 L33: 1.2784 L12: 0.6911 REMARK 3 L13: 0.5834 L23: 2.0226 REMARK 3 S TENSOR REMARK 3 S11: -0.2945 S12: -0.6267 S13: -0.1583 REMARK 3 S21: 0.8787 S22: 0.3193 S23: -0.2534 REMARK 3 S31: 1.1974 S32: 0.6061 S33: -0.0862 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9996 0.8621 10.1632 REMARK 3 T TENSOR REMARK 3 T11: 0.2221 T22: 0.4394 REMARK 3 T33: 0.9624 T12: 0.1611 REMARK 3 T13: 0.0018 T23: 0.0075 REMARK 3 L TENSOR REMARK 3 L11: 2.3152 L22: 2.6652 REMARK 3 L33: 2.6193 L12: -0.6653 REMARK 3 L13: -0.0406 L23: 0.2963 REMARK 3 S TENSOR REMARK 3 S11: -0.1656 S12: -0.0987 S13: -0.3719 REMARK 3 S21: 0.5639 S22: -0.1684 S23: -0.0162 REMARK 3 S31: 0.1393 S32: 0.1138 S33: 0.1659 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.7220 -8.8128 20.5271 REMARK 3 T TENSOR REMARK 3 T11: 0.6957 T22: 0.9350 REMARK 3 T33: 0.6999 T12: 0.3967 REMARK 3 T13: 0.0594 T23: 0.1789 REMARK 3 L TENSOR REMARK 3 L11: 1.9014 L22: 2.7998 REMARK 3 L33: 0.6878 L12: -2.0252 REMARK 3 L13: 0.6073 L23: -0.0353 REMARK 3 S TENSOR REMARK 3 S11: -0.0485 S12: -0.2673 S13: -0.1308 REMARK 3 S21: 0.9723 S22: 0.5518 S23: 0.5963 REMARK 3 S31: -0.2361 S32: -0.5546 S33: -0.4493 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 41 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5199 -49.4634 34.6085 REMARK 3 T TENSOR REMARK 3 T11: 1.0061 T22: 1.3156 REMARK 3 T33: 0.9114 T12: 0.1332 REMARK 3 T13: 0.1208 T23: 0.1824 REMARK 3 L TENSOR REMARK 3 L11: 4.5884 L22: 5.5582 REMARK 3 L33: 1.7885 L12: 2.6324 REMARK 3 L13: 1.0217 L23: -1.9373 REMARK 3 S TENSOR REMARK 3 S11: 0.2355 S12: -0.8668 S13: 0.4443 REMARK 3 S21: 1.4283 S22: 0.1095 S23: 0.1050 REMARK 3 S31: -1.0343 S32: -0.5458 S33: -0.3385 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 92 THROUGH 134 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1625 0.5150 9.9480 REMARK 3 T TENSOR REMARK 3 T11: 0.2731 T22: 0.8569 REMARK 3 T33: 0.7917 T12: 0.5235 REMARK 3 T13: 0.2453 T23: 0.2441 REMARK 3 L TENSOR REMARK 3 L11: 1.9031 L22: 1.4530 REMARK 3 L33: 0.6847 L12: -0.3576 REMARK 3 L13: 0.8368 L23: 0.2803 REMARK 3 S TENSOR REMARK 3 S11: -0.2443 S12: -0.5610 S13: -0.3261 REMARK 3 S21: 0.6475 S22: 0.3058 S23: -0.0317 REMARK 3 S31: 0.2197 S32: -0.2136 S33: -0.0955 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "A" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "B" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8UO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12674 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 57.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SPG (MIXTURE OF SUCCINIC ACID, REMARK 280 SODIUM DIHYDROGEN PHOSPHATE, AND GLYCINE IN A 2:7:7 MOLAR RATIO), REMARK 280 20-24% POLYETHYLENE GLYCOL-6000, AND 200 MM SODIUM FLUORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.65700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 IN SAME ASYMMETRIC UNIT 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 O2' U B 105 OP1 A B 108 2.08 REMARK 500 O2' G A 60 OP2 C A 62 2.11 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 G A 1 P G A 1 OP3 -0.126 REMARK 500 G B 1 P G B 1 OP3 -0.126 REMARK 500 REMARK 500 REMARK: NULL DBREF 8UO6 A 1 134 PDB 8UO6 8UO6 1 134 DBREF 8UO6 B 1 134 PDB 8UO6 8UO6 1 134 SEQRES 1 A 134 G C C C G G A U A G C U C SEQRES 2 A 134 A G U C G G U A G A G C A SEQRES 3 A 134 G C G G G C A C U A U G G SEQRES 4 A 134 G C G C A G U G U C A A U SEQRES 5 A 134 G G A C G C U G A C G G U SEQRES 6 A 134 A C A G G C C A G A C A A SEQRES 7 A 134 U U A U U G U C U G G U A SEQRES 8 A 134 U A G U G C C C G C G G G SEQRES 9 A 134 U C C A G G G U U C A A G SEQRES 10 A 134 U C C C U G U U C G G G C SEQRES 11 A 134 G C C A SEQRES 1 B 134 G C C C G G A U A G C U C SEQRES 2 B 134 A G U C G G U A G A G C A SEQRES 3 B 134 G C G G G C A C U A U G G SEQRES 4 B 134 G C G C A G U G U C A A U SEQRES 5 B 134 G G A C G C U G A C G G U SEQRES 6 B 134 A C A G G C C A G A C A A SEQRES 7 B 134 U U A U U G U C U G G U A SEQRES 8 B 134 U A G U G C C C G C G G G SEQRES 9 B 134 U C C A G G G U U C A A G SEQRES 10 B 134 U C C C U G U U C G G G C SEQRES 11 B 134 G C C A CRYST1 67.782 81.314 81.372 90.00 99.14 90.00 P 1 21 1 4 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 0.014753 0.000000 0.002374 0.00000 SCALE2 0.000000 0.012298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012447 0.00000 MTRIX1 1 -0.747372 0.100270 -0.656796 22.67379 1 MTRIX2 1 -0.076369 -0.994959 -0.064994 2.59151 1 MTRIX3 1 -0.660002 0.001584 0.751262 -3.31835 1