HEADER VIRAL PROTEIN 07-SEP-17 6AY9 TITLE STRUCTURE OF THE NATIVE FULL-LENGTH HIV-1 CAPSID PROTEIN IN COMPLEX TITLE 2 WITH CPSF6 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 CAPSID PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 133-363; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 276-287; COMPND 10 SYNONYM: CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 68 KDA COMPND 11 SUBUNIT,CPSF 68 KDA SUBUNIT,PRE-MRNA CLEAVAGE FACTOR IM 68 KDA COMPND 12 SUBUNIT,PROTEIN HPBRII-4/7; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS HIV-1 CAPSID PROTEIN, HEXAMER, CPSF6 COMPLEX, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.T.GRES,K.A.KIRBY,S.G.SARAFIANOS REVDAT 4 04-OCT-23 6AY9 1 JRNL REVDAT 3 11-DEC-19 6AY9 1 REMARK REVDAT 2 20-FEB-19 6AY9 1 REMARK REVDAT 1 12-SEP-18 6AY9 0 JRNL AUTH A.T.GRES,K.A.KIRBY,W.M.MCFADDEN,H.DU,D.LIU,C.XU,A.J.BRYER, JRNL AUTH 2 J.R.PERILLA,J.SHI,C.AIKEN,X.FU,P.ZHANG,A.C.FRANCIS, JRNL AUTH 3 G.B.MELIKYAN,S.G.SARAFIANOS JRNL TITL MULTIDISCIPLINARY STUDIES WITH MUTATED HIV-1 CAPSID PROTEINS JRNL TITL 2 REVEAL STRUCTURAL MECHANISMS OF LATTICE STABILIZATION. JRNL REF NAT COMMUN V. 14 5614 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37699872 JRNL DOI 10.1038/S41467-023-41197-7 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1-2575_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.010 REMARK 3 FREE R VALUE TEST SET COUNT : 598 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 47.0403 - 3.9682 1.00 2417 127 0.2164 0.2391 REMARK 3 2 3.9682 - 3.1499 1.00 2356 123 0.2359 0.2606 REMARK 3 3 3.1499 - 2.7518 1.00 2284 181 0.2913 0.3217 REMARK 3 4 2.7518 - 2.5002 1.00 2295 167 0.3561 0.3732 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 75.10 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 : 0.002 1839 REMARK 3 ANGLE : 0.496 2501 REMARK 3 CHIRALITY : 0.038 277 REMARK 3 PLANARITY : 0.004 326 REMARK 3 DIHEDRAL : 13.353 1128 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.8425 -12.3290 16.4250 REMARK 3 T TENSOR REMARK 3 T11: 0.6082 T22: 0.5789 REMARK 3 T33: 0.4241 T12: -0.1077 REMARK 3 T13: 0.0297 T23: 0.1516 REMARK 3 L TENSOR REMARK 3 L11: 0.0209 L22: -0.0278 REMARK 3 L33: 0.0220 L12: -0.0141 REMARK 3 L13: -0.0459 L23: -0.0120 REMARK 3 S TENSOR REMARK 3 S11: 0.4175 S12: -0.6137 S13: -0.8784 REMARK 3 S21: -0.1450 S22: 0.0793 S23: 0.3871 REMARK 3 S31: -0.0165 S32: 0.3877 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 17 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.6861 -16.8541 -3.5367 REMARK 3 T TENSOR REMARK 3 T11: 0.3889 T22: 0.4055 REMARK 3 T33: 0.4744 T12: -0.0461 REMARK 3 T13: 0.0926 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 0.0545 L22: 0.1406 REMARK 3 L33: 0.0798 L12: 0.1679 REMARK 3 L13: -0.0898 L23: 0.2230 REMARK 3 S TENSOR REMARK 3 S11: -0.0355 S12: 0.0368 S13: 0.4960 REMARK 3 S21: -0.0958 S22: 0.0277 S23: -0.6334 REMARK 3 S31: -0.0195 S32: 0.0248 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0178 -29.4171 3.9272 REMARK 3 T TENSOR REMARK 3 T11: 0.3770 T22: 0.3335 REMARK 3 T33: 0.4090 T12: -0.0219 REMARK 3 T13: 0.0579 T23: 0.0816 REMARK 3 L TENSOR REMARK 3 L11: -0.1222 L22: 0.4911 REMARK 3 L33: 0.5186 L12: -0.5277 REMARK 3 L13: 0.0365 L23: 0.1628 REMARK 3 S TENSOR REMARK 3 S11: -0.0978 S12: -0.0935 S13: -0.0973 REMARK 3 S21: 0.0661 S22: 0.0843 S23: -0.0837 REMARK 3 S31: 0.0995 S32: 0.2321 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 104 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.9677 -34.0980 23.4212 REMARK 3 T TENSOR REMARK 3 T11: 0.7638 T22: 0.4560 REMARK 3 T33: 0.7701 T12: -0.0767 REMARK 3 T13: 0.2426 T23: 0.0998 REMARK 3 L TENSOR REMARK 3 L11: -0.0091 L22: 0.0034 REMARK 3 L33: 0.0150 L12: 0.1059 REMARK 3 L13: -0.0151 L23: -0.0569 REMARK 3 S TENSOR REMARK 3 S11: -0.2041 S12: -0.1900 S13: -0.2595 REMARK 3 S21: -0.2422 S22: -0.6090 S23: 0.3298 REMARK 3 S31: 0.0368 S32: 0.1919 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 105 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6858 -24.4189 19.5162 REMARK 3 T TENSOR REMARK 3 T11: 0.8840 T22: 0.6774 REMARK 3 T33: 0.6967 T12: 0.0892 REMARK 3 T13: 0.2545 T23: -0.1178 REMARK 3 L TENSOR REMARK 3 L11: 0.0494 L22: 0.1575 REMARK 3 L33: 0.1341 L12: 0.1563 REMARK 3 L13: -0.1424 L23: -0.0772 REMARK 3 S TENSOR REMARK 3 S11: 0.0309 S12: -0.7211 S13: 0.5299 REMARK 3 S21: 0.6430 S22: 0.3623 S23: 1.1255 REMARK 3 S31: -0.0796 S32: 0.0322 S33: -0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 126 THROUGH 144 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0550 -29.7051 3.3586 REMARK 3 T TENSOR REMARK 3 T11: 0.3311 T22: 0.4613 REMARK 3 T33: 0.5699 T12: -0.0126 REMARK 3 T13: 0.0530 T23: 0.0668 REMARK 3 L TENSOR REMARK 3 L11: 0.0892 L22: 0.3069 REMARK 3 L33: 0.0586 L12: 0.1126 REMARK 3 L13: 0.0044 L23: -0.1805 REMARK 3 S TENSOR REMARK 3 S11: -0.0830 S12: -0.0772 S13: -0.1463 REMARK 3 S21: 0.2413 S22: -0.1395 S23: -0.4175 REMARK 3 S31: 0.2702 S32: -0.0753 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 145 THROUGH 160 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.4130 -29.1626 -18.8508 REMARK 3 T TENSOR REMARK 3 T11: 0.7694 T22: 0.6389 REMARK 3 T33: 0.4398 T12: 0.2009 REMARK 3 T13: -0.0776 T23: 0.0622 REMARK 3 L TENSOR REMARK 3 L11: -0.0474 L22: 0.2095 REMARK 3 L33: 0.3487 L12: 0.0165 REMARK 3 L13: 0.1293 L23: 0.2803 REMARK 3 S TENSOR REMARK 3 S11: -0.1547 S12: 0.2402 S13: 0.4173 REMARK 3 S21: -0.5098 S22: 0.2115 S23: 0.3696 REMARK 3 S31: 0.3029 S32: -0.2097 S33: 0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 161 THROUGH 174 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.4013 -24.3730 -12.9681 REMARK 3 T TENSOR REMARK 3 T11: 0.1077 T22: -0.3375 REMARK 3 T33: 0.2337 T12: 0.7411 REMARK 3 T13: -0.2480 T23: 0.8114 REMARK 3 L TENSOR REMARK 3 L11: 0.1055 L22: -0.0183 REMARK 3 L33: 0.1696 L12: 0.1276 REMARK 3 L13: 0.2264 L23: 0.0763 REMARK 3 S TENSOR REMARK 3 S11: 0.6525 S12: -0.7670 S13: 0.8183 REMARK 3 S21: 0.3643 S22: -2.3314 S23: 1.4635 REMARK 3 S31: 1.2063 S32: -1.5113 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 175 THROUGH 192 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5689 -34.7574 -6.7743 REMARK 3 T TENSOR REMARK 3 T11: 0.4838 T22: 0.4198 REMARK 3 T33: 0.3625 T12: 0.0830 REMARK 3 T13: 0.0016 T23: 0.0658 REMARK 3 L TENSOR REMARK 3 L11: 0.0380 L22: 0.3250 REMARK 3 L33: 0.0924 L12: 0.1032 REMARK 3 L13: -0.0256 L23: 0.0111 REMARK 3 S TENSOR REMARK 3 S11: -0.0802 S12: -0.2043 S13: 0.3353 REMARK 3 S21: -0.3132 S22: 0.0496 S23: -0.0857 REMARK 3 S31: 0.6608 S32: 0.1801 S33: 0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 193 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.2604 -28.6730 -18.2179 REMARK 3 T TENSOR REMARK 3 T11: 0.5512 T22: 0.9681 REMARK 3 T33: 0.8336 T12: 0.1672 REMARK 3 T13: -0.0281 T23: -0.0481 REMARK 3 L TENSOR REMARK 3 L11: -0.0031 L22: 0.0080 REMARK 3 L33: 0.0268 L12: 0.0329 REMARK 3 L13: 0.0093 L23: 0.0262 REMARK 3 S TENSOR REMARK 3 S11: -0.3405 S12: 0.3289 S13: -0.0039 REMARK 3 S21: -0.1985 S22: -0.1563 S23: -0.3320 REMARK 3 S31: 0.2721 S32: 0.2170 S33: 0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 206 THROUGH 221 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.8320 -21.8359 -11.3324 REMARK 3 T TENSOR REMARK 3 T11: 0.5483 T22: 0.7453 REMARK 3 T33: 0.7897 T12: 0.0582 REMARK 3 T13: 0.0588 T23: 0.1288 REMARK 3 L TENSOR REMARK 3 L11: 0.0293 L22: 0.0059 REMARK 3 L33: 0.1148 L12: -0.0379 REMARK 3 L13: -0.1003 L23: 0.1340 REMARK 3 S TENSOR REMARK 3 S11: -0.5152 S12: -0.3611 S13: 0.1820 REMARK 3 S21: -0.0513 S22: 0.2012 S23: -0.3716 REMARK 3 S31: 0.4753 S32: 1.0890 S33: -0.0000 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 313 THROUGH 324 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9718 -31.8672 3.1623 REMARK 3 T TENSOR REMARK 3 T11: 0.3678 T22: 0.6615 REMARK 3 T33: 0.1538 T12: -0.1554 REMARK 3 T13: 0.1110 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: -0.0133 L22: -0.0086 REMARK 3 L33: 0.0240 L12: 0.0536 REMARK 3 L13: -0.0017 L23: 0.0348 REMARK 3 S TENSOR REMARK 3 S11: -0.1933 S12: -0.7100 S13: -0.0492 REMARK 3 S21: 0.3033 S22: -0.4452 S23: 0.0402 REMARK 3 S31: 0.0894 S32: -0.6215 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6AY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229993. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033203 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS 0.5.32 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9956 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.17 REMARK 200 STARTING MODEL: 4XFX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, NAI, SODIUM CACODYLATE, REMARK 280 GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 34350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 60640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -410.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 5 REMARK 465 LEU A 6 REMARK 465 GLN A 7 REMARK 465 GLY A 222 REMARK 465 GLY A 223 REMARK 465 PRO A 224 REMARK 465 GLY A 225 REMARK 465 HIS A 226 REMARK 465 LYS A 227 REMARK 465 ALA A 228 REMARK 465 ARG A 229 REMARK 465 VAL A 230 REMARK 465 LEU A 231 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 ALA A 31 -118.16 49.70 REMARK 500 PHE A 32 60.27 -117.81 REMARK 500 PRO A 207 0.15 -69.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XFX RELATED DB: PDB REMARK 900 STRUCTURE OF THE NATIVE FULL-LENGTH HIV-1 CAPSID PROTEIN DBREF 6AY9 A 1 231 UNP B6DRA0 B6DRA0_9HIV1 133 363 DBREF 6AY9 B 313 324 UNP Q16630 CPSF6_HUMAN 276 287 SEQRES 1 A 231 PRO ILE VAL GLN ASN LEU GLN GLY GLN MET VAL HIS GLN SEQRES 2 A 231 ALA ILE SER PRO ARG THR LEU ASN ALA TRP VAL LYS VAL SEQRES 3 A 231 VAL GLU GLU LYS ALA PHE SER PRO GLU VAL ILE PRO MET SEQRES 4 A 231 PHE SER ALA LEU SER GLU GLY ALA THR PRO GLN ASP LEU SEQRES 5 A 231 ASN THR MET LEU ASN THR VAL GLY GLY HIS GLN ALA ALA SEQRES 6 A 231 MET GLN MET LEU LYS GLU THR ILE ASN GLU GLU ALA ALA SEQRES 7 A 231 GLU TRP ASP ARG LEU HIS PRO VAL HIS ALA GLY PRO ILE SEQRES 8 A 231 ALA PRO GLY GLN MET ARG GLU PRO ARG GLY SER ASP ILE SEQRES 9 A 231 ALA GLY THR THR SER THR LEU GLN GLU GLN ILE GLY TRP SEQRES 10 A 231 MET THR HIS ASN PRO PRO ILE PRO VAL GLY GLU ILE TYR SEQRES 11 A 231 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS ILE VAL ARG SEQRES 12 A 231 MET TYR SER PRO THR SER ILE LEU ASP ILE ARG GLN GLY SEQRES 13 A 231 PRO LYS GLU PRO PHE ARG ASP TYR VAL ASP ARG PHE TYR SEQRES 14 A 231 LYS THR LEU ARG ALA GLU GLN ALA SER GLN GLU VAL LYS SEQRES 15 A 231 ASN TRP MET THR GLU THR LEU LEU VAL GLN ASN ALA ASN SEQRES 16 A 231 PRO ASP CYS LYS THR ILE LEU LYS ALA LEU GLY PRO GLY SEQRES 17 A 231 ALA THR LEU GLU GLU MET MET THR ALA CYS GLN GLY VAL SEQRES 18 A 231 GLY GLY PRO GLY HIS LYS ALA ARG VAL LEU SEQRES 1 B 12 PRO VAL LEU PHE PRO GLY GLN PRO PHE GLY GLN PRO HET IOD A 301 1 HET IOD A 302 1 HET IOD A 303 1 HET IOD A 304 1 HET IOD A 305 1 HET IOD A 306 1 HET CL A 307 1 HET CL A 308 1 HET CL A 309 1 HET CL A 310 1 HETNAM IOD IODIDE ION HETNAM CL CHLORIDE ION FORMUL 3 IOD 6(I 1-) FORMUL 9 CL 4(CL 1-) FORMUL 13 HOH *31(H2 O) HELIX 1 AA1 SER A 16 ALA A 31 1 16 HELIX 2 AA2 GLU A 35 SER A 44 1 10 HELIX 3 AA3 THR A 48 THR A 58 1 11 HELIX 4 AA4 HIS A 62 HIS A 84 1 23 HELIX 5 AA5 ARG A 100 ALA A 105 1 6 HELIX 6 AA6 THR A 110 HIS A 120 1 11 HELIX 7 AA7 PRO A 125 TYR A 145 1 21 HELIX 8 AA8 SER A 149 ILE A 153 5 5 HELIX 9 AA9 PRO A 160 ALA A 174 1 15 HELIX 10 AB1 SER A 178 ASN A 193 1 16 HELIX 11 AB2 ASN A 195 GLY A 206 1 12 HELIX 12 AB3 THR A 210 CYS A 218 1 9 SHEET 1 AA1 2 ILE A 2 VAL A 3 0 SHEET 2 AA1 2 VAL A 11 HIS A 12 -1 O VAL A 11 N VAL A 3 SSBOND 1 CYS A 198 CYS A 218 1555 1555 2.04 CISPEP 1 ASN A 121 PRO A 122 0 3.95 SITE 1 AC1 1 ARG A 173 SITE 1 AC2 2 ALA A 92 GLN A 95 SITE 1 AC3 1 ARG A 18 SITE 1 AC4 1 TYR A 145 SITE 1 AC5 1 ARG A 18 SITE 1 AC6 2 PHE A 161 ARG A 162 SITE 1 AC7 1 ARG A 167 SITE 1 AC8 1 ASP A 152 SITE 1 AC9 2 PRO A 38 PRO B 320 CRYST1 92.675 92.675 58.042 90.00 90.00 120.00 P 6 6 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 0.010790 0.006230 0.000000 0.00000 SCALE2 0.000000 0.012460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017229 0.00000