HEADER RNA 18-FEB-20 6VVJ TITLE CAP1G-TPUA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (130-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, CAPPED RNA, VIRAL, MAL STRAIN, MAL, 5' LEADER, LEADER RNA, KEYWDS 2 COVERED CAP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.F.SUMMERS,J.D.BROWN REVDAT 4 06-MAR-24 6VVJ 1 COMPND FORMUL REVDAT 3 14-JUN-23 6VVJ 1 REMARK REVDAT 2 20-MAY-20 6VVJ 1 TITLE JRNL REVDAT 1 29-APR-20 6VVJ 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 6VVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000247079. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 10 MM KH2PO4, 1 MM MGCL2, 122 MM REMARK 210 KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 150 UM 1H CAP1G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM GH REMARK 210 CAP1G-TPUA, 10 MM DEUTERATED REMARK 210 KH2PO4, 1 MM MGCL2, 122 MM KCL, REMARK 210 100% D2O; 150 UM A2RGR CAP1G- REMARK 210 TPUA, 10 MM DEUTERATED KH2PO4, 1 REMARK 210 MM MGCL2, 122 MM KCL, 100% D2O; REMARK 210 150 UM GHU6R CAP1G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM U6R REMARK 210 CAP1G-TPUA, 10 MM DEUTERATED REMARK 210 KH2PO4, 1 MM MGCL2, 122 MM KCL, REMARK 210 100% D2O; 150 UM C6R CAP1G-TPUA, REMARK 210 10 MM DEUTERATED KH2PO4, 1 MM REMARK 210 MGCL2, 122 MM KCL, 100% D2O; 150 REMARK 210 UM C6RU6R CAP1G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM REMARK 210 AHCH CAP1G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM U6R REMARK 210 CAP1G-TPUA, 10 MM DEUTERATED REMARK 210 KH2PO4, 1 MM MGCL2, 122 MM KCL, REMARK 210 90% H2O/10% D2O; 150 UM 1H CAP1G- REMARK 210 TPUA, 10 MM DEUTERATED KH2PO4, 1 REMARK 210 MM MGCL2, 122 MM KCL, 90% H2O/10% REMARK 210 D2O; 150 UM GH CAP1G-TPUA, 10 REMARK 210 MM DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 90% H2O/10% D2O; REMARK 210 150 UM 1H 2G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM AH REMARK 210 2G-TPUA, 10 MM DEUTERATED KH2PO4, REMARK 210 1 MM MGCL2, 122 MM KCL, 100% REMARK 210 D2O; 150 UM CH 2G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM UH REMARK 210 2G-TPUA, 10 MM DEUTERATED KH2PO4, REMARK 210 1 MM MGCL2, 122 MM KCL, 100% REMARK 210 D2O; 150 UM A2RCR 2G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM REMARK 210 A2RUR 2G-TPUA, 10 MM DEUTERATED REMARK 210 KH2PO4, 1 MM MGCL2, 122 MM KCL, REMARK 210 100% D2O; 150 UM C6RUR 2G-TPUA, REMARK 210 10 MM DEUTERATED KH2PO4, 1 MM REMARK 210 MGCL2, 122 MM KCL, 100% D2O; 150 REMARK 210 UM CRU6R 2G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM REMARK 210 AHCH 2G-TPUA, 10 MM DEUTERATED REMARK 210 KH2PO4, 1 MM MGCL2, 122 MM KCL, REMARK 210 100% D2O; 150 UM CHGH 2G-TPUA, REMARK 210 10 MM DEUTERATED KH2PO4, 1 MM REMARK 210 MGCL2, 122 MM KCL, 100% D2O; 150 REMARK 210 UM GHUH 2G-TPUA, 10 MM REMARK 210 DEUTERATED KH2PO4, 1 MM MGCL2, REMARK 210 122 MM KCL, 100% D2O; 150 UM REMARK 210 AHUH 2G-TPUA, 10 MM DEUTERATED REMARK 210 KH2PO4, 1 MM MGCL2, 122 MM KCL, REMARK 210 100% D2O; 150 UM AHGH 2G-TPUA, REMARK 210 10 MM DEUTERATED KH2PO4, 1 MM REMARK 210 MGCL2, 122 M KCL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFX, NMRVIEW, CYANA, AMBER 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 HO3' M7G A 2 OP2 G A 3 1.49 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 3 C5' - C4' - O4' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 7 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 9 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 15 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 A A 17 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 17 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 17 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 C A 18 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 19 N3 - C2 - O2 ANGL. DEV. = -4.6 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. = -4.2 DEGREES REMARK 500 1 C A 24 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 26 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 26 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 26 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 28 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 34 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 A A 34 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 34 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 C A 36 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 C A 38 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 40 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 44 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 A A 46 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 46 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 46 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 C A 48 N3 - C2 - O2 ANGL. DEV. = -4.6 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. = 3.7 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. = -3.1 DEGREES REMARK 500 1 A A 50 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 50 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 53 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 53 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 53 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 A A 54 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 54 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 C A 55 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 56 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 57 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 58 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 58 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 58 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 59 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 62 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 65 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 2162 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30724 RELATED DB: BMRB REMARK 900 CAP3G-TAR-F1 DBREF 6VVJ A 2 359 PDB 6VVJ 6VVJ 2 359 SEQRES 1 A 130 M7G G U C U C U C U U G U U SEQRES 2 A 130 A G A C C A G G U C G A G SEQRES 3 A 130 C C C G G G A G C U C U C SEQRES 4 A 130 U G G C U A G C A A G G A SEQRES 5 A 130 A C C C A C U G C U U A A SEQRES 6 A 130 G C C U C A A U A A A G C SEQRES 7 A 130 U U G C C U U G A G U G C SEQRES 8 A 130 C U C A A G C A G U G U G SEQRES 9 A 130 U G C C C A U C U C G A G SEQRES 10 A 130 A G A G A U G G G U G C G HET M7G A 2 44 HETNAM M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE FORMUL 1 M7G C11 H18 N5 O11 P2 1+ LINK O3B M7G A 2 P G A 3 1555 1555 1.55 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 2 -18.762 20.958 -5.075 1.00 0.00 P HETATM 2 O1A M7G A 2 -18.062 21.966 -5.899 1.00 0.00 O HETATM 3 O2A M7G A 2 -20.076 20.465 -5.533 1.00 0.00 O HETATM 4 O3A M7G A 2 -18.810 21.466 -3.649 1.00 0.00 O HETATM 5 O5' M7G A 2 -17.765 19.703 -4.997 1.00 0.00 O HETATM 6 PB M7G A 2 -19.982 21.728 -2.712 1.00 0.00 P HETATM 7 O1B M7G A 2 -20.692 22.941 -3.171 1.00 0.00 O HETATM 8 O2B M7G A 2 -20.772 20.486 -2.563 1.00 0.00 O HETATM 9 O3B M7G A 2 -19.359 22.010 -1.314 1.00 0.00 O HETATM 10 C5' M7G A 2 -18.060 18.556 -4.195 1.00 0.00 C HETATM 11 C4' M7G A 2 -17.032 18.315 -3.075 1.00 0.00 C HETATM 12 O4' M7G A 2 -15.801 17.771 -3.553 1.00 0.00 O HETATM 13 C3' M7G A 2 -16.618 19.568 -2.306 1.00 0.00 C HETATM 14 O3' M7G A 2 -17.542 20.066 -1.357 1.00 0.00 O HETATM 15 C2' M7G A 2 -15.368 19.066 -1.596 1.00 0.00 C HETATM 16 O2' M7G A 2 -15.679 18.249 -0.475 1.00 0.00 O HETATM 17 C1' M7G A 2 -14.742 18.213 -2.696 1.00 0.00 C HETATM 18 N9 M7G A 2 -13.781 19.043 -3.459 1.00 0.00 N HETATM 19 C8 M7G A 2 -13.889 19.489 -4.751 1.00 0.00 C HETATM 20 N7 M7G A 2 -12.739 20.251 -5.084 1.00 0.00 N HETATM 21 CM7 M7G A 2 -12.561 20.835 -6.455 1.00 0.00 C HETATM 22 C5 M7G A 2 -11.979 20.261 -3.939 1.00 0.00 C HETATM 23 C6 M7G A 2 -10.730 20.857 -3.649 1.00 0.00 C HETATM 24 O6 M7G A 2 -10.005 21.513 -4.377 1.00 0.00 O HETATM 25 N1 M7G A 2 -10.333 20.690 -2.373 1.00 0.00 N HETATM 26 C2 M7G A 2 -11.022 20.005 -1.491 1.00 0.00 C HETATM 27 N2 M7G A 2 -10.545 19.936 -0.310 1.00 0.00 N HETATM 28 N3 M7G A 2 -12.160 19.402 -1.693 1.00 0.00 N HETATM 29 C4 M7G A 2 -12.600 19.555 -2.955 1.00 0.00 C HETATM 30 H5'1 M7G A 2 -18.097 17.670 -4.830 1.00 0.00 H HETATM 31 H5'2 M7G A 2 -19.044 18.664 -3.732 1.00 0.00 H HETATM 32 H4' M7G A 2 -17.466 17.609 -2.364 1.00 0.00 H HETATM 33 H3' M7G A 2 -16.336 20.346 -3.019 1.00 0.00 H HETATM 34 HO3' M7G A 2 -17.305 21.025 -1.336 1.00 0.00 H HETATM 35 H2' M7G A 2 -14.729 19.905 -1.320 1.00 0.00 H HETATM 36 HO2' M7G A 2 -16.414 18.687 -0.012 1.00 0.00 H HETATM 37 H1' M7G A 2 -14.215 17.364 -2.251 1.00 0.00 H HETATM 38 H81 M7G A 2 -14.730 19.270 -5.393 1.00 0.00 H HETATM 39 HM71 M7G A 2 -11.498 20.931 -6.682 1.00 0.00 H HETATM 40 HM72 M7G A 2 -13.013 21.827 -6.494 1.00 0.00 H HETATM 41 HM73 M7G A 2 -13.025 20.203 -7.213 1.00 0.00 H HETATM 42 HN1 M7G A 2 -9.454 21.094 -2.102 1.00 0.00 H HETATM 43 HN21 M7G A 2 -9.676 20.391 -0.061 1.00 0.00 H HETATM 44 HN22 M7G A 2 -11.086 19.406 0.347 1.00 0.00 H