HEADER RNA 14-FEB-20 6VU1 TITLE CAP3G-TAR-F1 IS AN RNA HAIRPIN. THE 1H-1H NOESY DATA WAS COLLECTED AT TITLE 2 308 K IN 10 MM KH2PO4 PH 7.4. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (34-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676 KEYWDS RNA, VIRUS, CAPPED RNA, VIRAL, NUCLEOTIDES, LEADER RNA, HIV GENOME, KEYWDS 2 GENOME, RNA GENOME, START SITE EXPOSED CAP, FREE CAP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.F.SUMMERS,J.D.BROWN REVDAT 5 15-MAY-24 6VU1 1 REMARK REVDAT 4 28-FEB-24 6VU1 1 REMARK SEQRES HET HETNAM REVDAT 4 2 1 FORMUL LINK ATOM REVDAT 3 14-JUN-23 6VU1 1 REMARK REVDAT 2 20-MAY-20 6VU1 1 JRNL REVDAT 1 29-APR-20 6VU1 0 JRNL AUTH J.D.BROWN,S.KHARYTONCHYK,I.CHAUDRY,A.S.IYER,H.CARTER, JRNL AUTH 2 G.BECKER,Y.DESAI,L.GLANG,S.H.CHOI,K.SINGH,M.W.LOPRESTI, JRNL AUTH 3 M.ORELLANA,T.RODRIGUEZ,U.OBOH,J.HIJJI,F.G.GHINGER,K.STEWART, JRNL AUTH 4 D.FRANCIS,B.EDWARDS,P.CHEN,D.A.CASE,A.TELESNITSKY, JRNL AUTH 5 M.F.SUMMERS JRNL TITL STRUCTURAL BASIS FOR TRANSCRIPTIONAL START SITE CONTROL OF JRNL TITL 2 HIV-1 RNA FATE. JRNL REF SCIENCE V. 368 413 2020 JRNL REFN ESSN 1095-9203 JRNL PMID 32327595 JRNL DOI 10.1126/SCIENCE.AAZ7959 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, CYANA REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN (AMBER), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE GEOMETRY, MOLECULAR DYNAMICS REMARK 4 REMARK 4 6VU1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000246636. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 308 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 10; 10 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 150 UM FULLY PROTONATED CAP3G REMARK 210 -TAR-F1, 10 MM DEUTERATED KH2PO4, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY 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 : CYANA, NMRVIEW, NMRFX REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 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 C A 7 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 14 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 A A 16 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 16 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 A A 18 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 18 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 18 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 C A 48 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 49 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 49 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 49 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 50 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 50 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 50 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 53 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 53 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A A 53 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 A A 54 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 54 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 55 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 56 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 57 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 58 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 58 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 58 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 C A 59 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 C A 7 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 C A 14 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 A A 16 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 16 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 A A 18 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 18 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 18 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 C A 48 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 A A 49 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 49 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 49 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 A A 50 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 50 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 50 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 A A 53 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 53 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 53 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 54 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 A A 54 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 54 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 558 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30723 RELATED DB: BMRB REMARK 900 CAP3G-TAR-F1 DBREF 6VU1 A 0 60 PDB 6VU1 6VU1 0 60 SEQRES 1 A 34 M7G G G G U C U C U C U U G SEQRES 2 A 34 U C G A G A G G C A A G G SEQRES 3 A 34 A A C C C A C U HET M7G A 0 44 HETNAM M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE FORMUL 1 M7G C11 H18 N5 O11 P2 1+ LINK O3B M7G A 0 P G A 1 1555 1555 1.58 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 HETATM 1 PA M7G A 0 -41.688 7.564 -9.062 1.00 0.00 P HETATM 2 O1A M7G A 0 -40.533 8.489 -8.991 1.00 0.00 O HETATM 3 O2A M7G A 0 -42.229 7.353 -10.423 1.00 0.00 O HETATM 4 O3A M7G A 0 -42.818 8.300 -8.260 1.00 0.00 O HETATM 5 O5' M7G A 0 -41.084 6.116 -8.579 1.00 0.00 O HETATM 6 PB M7G A 0 -43.177 7.420 -7.074 1.00 0.00 P HETATM 7 O1B M7G A 0 -43.842 6.244 -7.662 1.00 0.00 O HETATM 8 O2B M7G A 0 -41.961 7.323 -6.241 1.00 0.00 O HETATM 9 O3B M7G A 0 -44.246 7.991 -6.148 1.00 0.00 O HETATM 10 C5' M7G A 0 -41.683 4.849 -8.907 1.00 0.00 C HETATM 11 C4' M7G A 0 -41.666 3.791 -7.769 1.00 0.00 C HETATM 12 O4' M7G A 0 -40.382 3.183 -7.657 1.00 0.00 O HETATM 13 C3' M7G A 0 -42.037 4.225 -6.330 1.00 0.00 C HETATM 14 O3' M7G A 0 -43.438 4.402 -6.063 1.00 0.00 O HETATM 15 C2' M7G A 0 -41.482 3.040 -5.532 1.00 0.00 C HETATM 16 O2' M7G A 0 -42.408 1.962 -5.529 1.00 0.00 O HETATM 17 C1' M7G A 0 -40.241 2.644 -6.345 1.00 0.00 C HETATM 18 N9 M7G A 0 -39.003 3.178 -5.722 1.00 0.00 N HETATM 19 C8 M7G A 0 -38.539 4.474 -5.711 1.00 0.00 C HETATM 20 N7 M7G A 0 -37.313 4.531 -5.001 1.00 0.00 N HETATM 21 CM7 M7G A 0 -36.578 5.829 -4.830 1.00 0.00 C HETATM 22 C5 M7G A 0 -37.075 3.239 -4.601 1.00 0.00 C HETATM 23 C6 M7G A 0 -36.006 2.682 -3.862 1.00 0.00 C HETATM 24 O6 M7G A 0 -35.018 3.240 -3.397 1.00 0.00 O HETATM 25 N1 M7G A 0 -36.124 1.355 -3.668 1.00 0.00 N HETATM 26 C2 M7G A 0 -37.132 0.646 -4.117 1.00 0.00 C HETATM 27 N2 M7G A 0 -37.067 -0.598 -3.833 1.00 0.00 N HETATM 28 N3 M7G A 0 -38.161 1.083 -4.807 1.00 0.00 N HETATM 29 C4 M7G A 0 -38.079 2.416 -5.025 1.00 0.00 C HETATM 30 H5'1 M7G A 0 -41.142 4.425 -9.754 1.00 0.00 H HETATM 31 H5'2 M7G A 0 -42.710 4.976 -9.250 1.00 0.00 H HETATM 32 H4' M7G A 0 -42.369 3.007 -8.052 1.00 0.00 H HETATM 33 H3' M7G A 0 -41.468 5.107 -6.061 1.00 0.00 H HETATM 34 HO3' M7G A 0 -43.716 5.109 -6.706 1.00 0.00 H HETATM 35 H2' M7G A 0 -41.230 3.340 -4.511 1.00 0.00 H HETATM 36 HO2' M7G A 0 -43.288 2.381 -5.521 1.00 0.00 H HETATM 37 H1' M7G A 0 -40.174 1.552 -6.385 1.00 0.00 H HETATM 38 H81 M7G A 0 -39.043 5.308 -6.179 1.00 0.00 H HETATM 39 HM71 M7G A 0 -35.671 5.668 -4.247 1.00 0.00 H HETATM 40 HM72 M7G A 0 -37.207 6.548 -4.308 1.00 0.00 H HETATM 41 HM73 M7G A 0 -36.301 6.231 -5.805 1.00 0.00 H HETATM 42 HN1 M7G A 0 -35.411 0.874 -3.154 1.00 0.00 H HETATM 43 HN21 M7G A 0 -36.265 -0.916 -3.302 1.00 0.00 H HETATM 44 HN22 M7G A 0 -37.813 -1.182 -4.153 1.00 0.00 H