HEADER PROTEIN BINDING 28-JUN-24 9IKQ TITLE CRYSTAL STRUCTURE OF OPTN LZD IN COMPLEX WITH GTP-BOUND RAB8A(Q67L) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-8A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ONCOGENE C-MEL; COMPND 5 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: OPTINEURIN; COMPND 10 CHAIN: C, D; COMPND 11 SYNONYM: E3-14.7K-INTERACTING PROTEIN,FIP-2,HUNTINGTIN YEAST PARTNER COMPND 12 L,HUNTINGTIN-INTERACTING PROTEIN 7,HIP-7,HUNTINGTIN-INTERACTING COMPND 13 PROTEIN L,NEMO-RELATED PROTEIN,OPTIC NEUROPATHY-INDUCING PROTEIN, COMPND 14 TRANSCRIPTION FACTOR IIIA-INTERACTING PROTEIN,TFIIIA-INTP; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB8A, MEL, RAB8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: OPTN, FIP2, GLC1E, HIP7, HYPL, NRP; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAB8A, OPTINEURIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.ZHANG,L.F.PAN REVDAT 1 25-DEC-24 9IKQ 0 JRNL AUTH J.ZHANG,L.LIU,M.LI,H.LIU,X.GONG,Y.TANG,Y.ZHANG,X.ZHOU,Z.LIN, JRNL AUTH 2 H.GUO,L.PAN JRNL TITL MOLECULAR BASIS OF THE RECOGNITION OF THE ACTIVE RAB8A BY JRNL TITL 2 OPTINEURIN. JRNL REF J.MOL.BIOL. V. 436 68811 2024 JRNL REFN ESSN 1089-8638 JRNL PMID 39374890 JRNL DOI 10.1016/J.JMB.2024.168811 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 37399 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1816 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 43.1900 - 4.5400 0.88 2708 155 0.1598 0.1925 REMARK 3 2 4.5300 - 3.6000 0.92 2742 120 0.1393 0.1678 REMARK 3 3 3.6000 - 3.1500 0.93 2693 165 0.1647 0.2143 REMARK 3 4 3.1400 - 2.8600 0.95 2771 114 0.1742 0.2373 REMARK 3 5 2.8600 - 2.6500 0.95 2786 119 0.1800 0.2146 REMARK 3 6 2.6500 - 2.5000 0.94 2712 131 0.1833 0.2678 REMARK 3 7 2.5000 - 2.3700 0.96 2721 173 0.1779 0.2322 REMARK 3 8 2.3700 - 2.2700 0.97 2767 161 0.1797 0.2359 REMARK 3 9 2.2700 - 2.1800 0.97 2785 140 0.1944 0.2446 REMARK 3 10 2.1800 - 2.1100 0.96 2711 144 0.1971 0.2322 REMARK 3 11 2.1100 - 2.0400 0.97 2796 119 0.2123 0.2495 REMARK 3 12 2.0400 - 1.9800 0.98 2835 119 0.2383 0.2680 REMARK 3 13 1.9800 - 1.9300 0.91 2556 156 0.2699 0.3012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.239 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.653 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.25 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 : 0.009 3658 REMARK 3 ANGLE : 1.052 4915 REMARK 3 CHIRALITY : 0.057 544 REMARK 3 PLANARITY : 0.004 617 REMARK 3 DIHEDRAL : 14.264 505 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 17 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4384 22.1185 -28.7446 REMARK 3 T TENSOR REMARK 3 T11: 0.2094 T22: 0.1438 REMARK 3 T33: 0.1416 T12: 0.0017 REMARK 3 T13: 0.0155 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 3.4826 L22: 2.5932 REMARK 3 L33: 2.8585 L12: 0.2925 REMARK 3 L13: 0.6455 L23: 0.6274 REMARK 3 S TENSOR REMARK 3 S11: 0.0109 S12: 0.1141 S13: 0.3501 REMARK 3 S21: -0.0889 S22: -0.0406 S23: 0.0598 REMARK 3 S31: -0.4150 S32: -0.0025 S33: 0.0421 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 43 THROUGH 52 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.2275 27.7858 -27.1311 REMARK 3 T TENSOR REMARK 3 T11: 0.2764 T22: 0.1352 REMARK 3 T33: 0.2812 T12: 0.0003 REMARK 3 T13: 0.0178 T23: 0.0141 REMARK 3 L TENSOR REMARK 3 L11: 4.5646 L22: 3.9429 REMARK 3 L33: 3.5560 L12: 0.7738 REMARK 3 L13: 0.3419 L23: 0.2289 REMARK 3 S TENSOR REMARK 3 S11: 0.2307 S12: -0.2643 S13: 0.3171 REMARK 3 S21: 0.2634 S22: -0.0258 S23: -0.8339 REMARK 3 S31: -0.6060 S32: -0.1039 S33: 0.0621 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 53 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4976 26.7881 -24.9496 REMARK 3 T TENSOR REMARK 3 T11: 0.2376 T22: 0.2141 REMARK 3 T33: 0.1868 T12: -0.0331 REMARK 3 T13: 0.0042 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 6.2021 L22: 5.3265 REMARK 3 L33: 6.5313 L12: 1.8377 REMARK 3 L13: 2.4430 L23: 2.2462 REMARK 3 S TENSOR REMARK 3 S11: -0.0725 S12: -0.1754 S13: 0.2837 REMARK 3 S21: 0.0042 S22: 0.0849 S23: -0.5522 REMARK 3 S31: -0.7160 S32: 0.2624 S33: -0.0159 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.9789 10.9771 -29.3871 REMARK 3 T TENSOR REMARK 3 T11: 0.1498 T22: 0.1337 REMARK 3 T33: 0.1373 T12: 0.0220 REMARK 3 T13: -0.0176 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 3.3187 L22: 2.7397 REMARK 3 L33: 3.5688 L12: 0.1655 REMARK 3 L13: -1.5340 L23: 0.0119 REMARK 3 S TENSOR REMARK 3 S11: 0.0198 S12: -0.0581 S13: 0.0225 REMARK 3 S21: -0.1033 S22: -0.0791 S23: -0.2275 REMARK 3 S31: -0.0180 S32: 0.1723 S33: 0.0650 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1949 3.6748 -23.4752 REMARK 3 T TENSOR REMARK 3 T11: 0.2069 T22: 0.1808 REMARK 3 T33: 0.1713 T12: 0.0310 REMARK 3 T13: 0.0081 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.7850 L22: 4.0715 REMARK 3 L33: 3.8971 L12: -0.2408 REMARK 3 L13: -1.8076 L23: -0.1357 REMARK 3 S TENSOR REMARK 3 S11: -0.0550 S12: -0.1914 S13: -0.5142 REMARK 3 S21: 0.1861 S22: -0.0660 S23: 0.0766 REMARK 3 S31: 0.2126 S32: 0.1367 S33: 0.1249 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 110 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5642 12.4450 -18.9084 REMARK 3 T TENSOR REMARK 3 T11: 0.2009 T22: 0.1756 REMARK 3 T33: 0.1406 T12: -0.0051 REMARK 3 T13: 0.0047 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.7680 L22: 2.8223 REMARK 3 L33: 3.3986 L12: -1.1933 REMARK 3 L13: -0.8093 L23: -0.0139 REMARK 3 S TENSOR REMARK 3 S11: -0.0523 S12: -0.2397 S13: -0.0056 REMARK 3 S21: 0.2202 S22: -0.0161 S23: 0.1055 REMARK 3 S31: -0.1205 S32: -0.1580 S33: 0.0563 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.5030 6.3844 -10.8068 REMARK 3 T TENSOR REMARK 3 T11: 0.2587 T22: 0.2811 REMARK 3 T33: 0.1462 T12: 0.0165 REMARK 3 T13: 0.0177 T23: -0.0187 REMARK 3 L TENSOR REMARK 3 L11: 2.2023 L22: 3.0592 REMARK 3 L33: 4.3007 L12: -0.2622 REMARK 3 L13: 0.6453 L23: -1.9745 REMARK 3 S TENSOR REMARK 3 S11: -0.1123 S12: -0.5235 S13: -0.0978 REMARK 3 S21: 0.5667 S22: 0.0473 S23: 0.0849 REMARK 3 S31: -0.2479 S32: -0.0853 S33: 0.0435 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 144 THROUGH 177 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.9611 21.3593 -15.7523 REMARK 3 T TENSOR REMARK 3 T11: 0.3116 T22: 0.2512 REMARK 3 T33: 0.1835 T12: -0.0457 REMARK 3 T13: -0.0140 T23: -0.0364 REMARK 3 L TENSOR REMARK 3 L11: 2.5427 L22: 2.7598 REMARK 3 L33: 1.4623 L12: -0.3303 REMARK 3 L13: 0.3147 L23: -0.1844 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: -0.2798 S13: 0.2028 REMARK 3 S21: 0.3716 S22: -0.0139 S23: -0.2455 REMARK 3 S31: -0.2454 S32: 0.1960 S33: 0.0290 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 134 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.7397 35.8227 -38.0332 REMARK 3 T TENSOR REMARK 3 T11: 0.4603 T22: 0.8328 REMARK 3 T33: 1.2481 T12: 0.0897 REMARK 3 T13: 0.0168 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 3.4977 L22: 9.5113 REMARK 3 L33: 7.6483 L12: 1.1876 REMARK 3 L13: -0.3849 L23: -2.9878 REMARK 3 S TENSOR REMARK 3 S11: 0.6144 S12: 0.7950 S13: -2.9450 REMARK 3 S21: -0.3910 S22: -0.2305 S23: 0.9640 REMARK 3 S31: 0.7833 S32: -1.1756 S33: -0.5000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 140 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.8276 29.9503 -38.8920 REMARK 3 T TENSOR REMARK 3 T11: 0.2654 T22: 0.1835 REMARK 3 T33: 0.1567 T12: -0.0463 REMARK 3 T13: 0.0381 T23: 0.0413 REMARK 3 L TENSOR REMARK 3 L11: 8.7848 L22: 6.6263 REMARK 3 L33: 3.4245 L12: -3.4730 REMARK 3 L13: -1.2246 L23: -0.4179 REMARK 3 S TENSOR REMARK 3 S11: 0.2730 S12: -0.2757 S13: 0.4600 REMARK 3 S21: 0.1407 S22: -0.0532 S23: -0.0101 REMARK 3 S31: -0.3078 S32: 0.0670 S33: -0.1430 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 136 THROUGH 170 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.2787 27.1026 -44.0283 REMARK 3 T TENSOR REMARK 3 T11: 0.1878 T22: 0.2239 REMARK 3 T33: 0.1823 T12: -0.0166 REMARK 3 T13: 0.0887 T23: 0.0438 REMARK 3 L TENSOR REMARK 3 L11: 6.0942 L22: 6.2293 REMARK 3 L33: 4.7270 L12: -2.5841 REMARK 3 L13: 0.2059 L23: -1.1126 REMARK 3 S TENSOR REMARK 3 S11: 0.2085 S12: 0.3180 S13: 0.2631 REMARK 3 S21: -0.1233 S22: -0.0881 S23: 0.2380 REMARK 3 S31: -0.3057 S32: -0.2988 S33: -0.0800 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7706 35.2086 -53.7079 REMARK 3 T TENSOR REMARK 3 T11: 0.1246 T22: 0.1980 REMARK 3 T33: 0.1747 T12: 0.0129 REMARK 3 T13: 0.0182 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 2.8851 L22: 3.3846 REMARK 3 L33: 3.1944 L12: -0.0507 REMARK 3 L13: 0.3403 L23: 0.5534 REMARK 3 S TENSOR REMARK 3 S11: -0.0240 S12: -0.0316 S13: -0.0660 REMARK 3 S21: 0.1293 S22: 0.0092 S23: 0.4231 REMARK 3 S31: -0.1458 S32: -0.4706 S33: 0.0109 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 43 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7732 27.3799 -56.7018 REMARK 3 T TENSOR REMARK 3 T11: 0.1695 T22: 0.2349 REMARK 3 T33: 0.2242 T12: -0.0300 REMARK 3 T13: 0.0150 T23: 0.0239 REMARK 3 L TENSOR REMARK 3 L11: 4.8403 L22: 4.6591 REMARK 3 L33: 5.5182 L12: 0.4009 REMARK 3 L13: 0.5019 L23: 0.9271 REMARK 3 S TENSOR REMARK 3 S11: -0.1198 S12: 0.2997 S13: -0.4831 REMARK 3 S21: -0.0750 S22: 0.0773 S23: 0.4576 REMARK 3 S31: 0.0583 S32: -0.5769 S33: 0.0080 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 65 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.7400 31.9129 -53.1420 REMARK 3 T TENSOR REMARK 3 T11: 0.1468 T22: 0.1667 REMARK 3 T33: 0.1817 T12: 0.0377 REMARK 3 T13: 0.0177 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 2.5818 L22: 1.6007 REMARK 3 L33: 3.8171 L12: 0.2395 REMARK 3 L13: 0.0767 L23: 0.0353 REMARK 3 S TENSOR REMARK 3 S11: -0.0456 S12: -0.1260 S13: -0.1416 REMARK 3 S21: 0.0446 S22: 0.0346 S23: -0.0887 REMARK 3 S31: 0.1730 S32: 0.1272 S33: 0.0109 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 93 THROUGH 121 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1013 31.1569 -60.8044 REMARK 3 T TENSOR REMARK 3 T11: 0.1564 T22: 0.1721 REMARK 3 T33: 0.0973 T12: 0.0280 REMARK 3 T13: 0.0355 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 4.8681 L22: 7.9265 REMARK 3 L33: 3.6601 L12: -1.4889 REMARK 3 L13: -0.7734 L23: -0.0490 REMARK 3 S TENSOR REMARK 3 S11: -0.0258 S12: 0.0929 S13: -0.2563 REMARK 3 S21: 0.0980 S22: -0.0200 S23: -0.1709 REMARK 3 S31: 0.1974 S32: 0.1262 S33: 0.0397 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 122 THROUGH 143 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0965 44.2586 -67.7071 REMARK 3 T TENSOR REMARK 3 T11: 0.2355 T22: 0.2167 REMARK 3 T33: 0.1877 T12: -0.0150 REMARK 3 T13: 0.0004 T23: 0.0631 REMARK 3 L TENSOR REMARK 3 L11: 4.0191 L22: 2.7046 REMARK 3 L33: 4.3021 L12: -1.3296 REMARK 3 L13: -1.7548 L23: 1.3814 REMARK 3 S TENSOR REMARK 3 S11: 0.2155 S12: 0.3775 S13: 0.4480 REMARK 3 S21: -0.3744 S22: -0.1677 S23: -0.1961 REMARK 3 S31: -0.5663 S32: -0.0683 S33: -0.1387 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 144 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2757 30.1210 -67.0927 REMARK 3 T TENSOR REMARK 3 T11: 0.1702 T22: 0.3023 REMARK 3 T33: 0.1520 T12: -0.0135 REMARK 3 T13: -0.0174 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.3658 L22: 2.7505 REMARK 3 L33: 2.1279 L12: 0.1439 REMARK 3 L13: -0.6354 L23: 0.1975 REMARK 3 S TENSOR REMARK 3 S11: -0.0794 S12: 0.4077 S13: -0.1517 REMARK 3 S21: -0.1023 S22: 0.0609 S23: 0.2018 REMARK 3 S31: 0.2323 S32: -0.3550 S33: 0.0437 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 9IKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98655 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 57.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.89900 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: PHENIX REMARK 200 STARTING MODEL: 4LHW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 16% (W/V) PEG REMARK 280 10000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 33.60900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.16850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.71600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.16850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.60900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.71600 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLU A 178 REMARK 465 GLY A 179 REMARK 465 ASN A 180 REMARK 465 SER A 181 REMARK 465 ARG C 133 REMARK 465 ARG D 133 REMARK 465 ALA D 134 REMARK 465 GLU D 135 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASN B 180 REMARK 465 SER B 181 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 O HOH B 382 O HOH B 452 2.19 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 LYS C 140 CB - CG - CD ANGL. DEV. = -22.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 30 15.16 -140.32 REMARK 500 VAL A 125 55.37 -96.63 REMARK 500 ASN A 155 65.71 61.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 471 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 472 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 473 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH B 477 DISTANCE = 6.06 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 87.4 REMARK 620 3 GTP A 201 O1G 176.4 89.5 REMARK 620 4 GTP A 201 O2B 90.7 172.9 92.7 REMARK 620 5 HOH A 303 O 87.6 83.3 93.8 89.9 REMARK 620 6 HOH A 321 O 86.0 97.7 92.6 88.9 173.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 206 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 22 OG1 REMARK 620 2 THR B 40 OG1 84.1 REMARK 620 3 GTP B 201 O1G 173.8 89.7 REMARK 620 4 GTP B 201 O2B 92.8 176.9 93.4 REMARK 620 5 HOH B 321 O 89.3 93.3 90.7 87.3 REMARK 620 6 HOH B 347 O 92.0 88.1 88.1 91.4 178.2 REMARK 620 N 1 2 3 4 5 DBREF 9IKQ A 1 181 UNP P61006 RAB8A_HUMAN 1 181 DBREF 9IKQ C 133 170 UNP Q96CV9 OPTN_HUMAN 133 170 DBREF 9IKQ D 133 170 UNP Q96CV9 OPTN_HUMAN 133 170 DBREF 9IKQ B 1 181 UNP P61006 RAB8A_HUMAN 1 181 SEQADV 9IKQ LEU A 67 UNP P61006 GLN 67 ENGINEERED MUTATION SEQADV 9IKQ LEU B 67 UNP P61006 GLN 67 ENGINEERED MUTATION SEQRES 1 A 181 MET ALA LYS THR TYR ASP TYR LEU PHE LYS LEU LEU LEU SEQRES 2 A 181 ILE GLY ASP SER GLY VAL GLY LYS THR CYS VAL LEU PHE SEQRES 3 A 181 ARG PHE SER GLU ASP ALA PHE ASN SER THR PHE ILE SER SEQRES 4 A 181 THR ILE GLY ILE ASP PHE LYS ILE ARG THR ILE GLU LEU SEQRES 5 A 181 ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP ASP THR ALA SEQRES 6 A 181 GLY LEU GLU ARG PHE ARG THR ILE THR THR ALA TYR TYR SEQRES 7 A 181 ARG GLY ALA MET GLY ILE MET LEU VAL TYR ASP ILE THR SEQRES 8 A 181 ASN GLU LYS SER PHE ASP ASN ILE ARG ASN TRP ILE ARG SEQRES 9 A 181 ASN ILE GLU GLU HIS ALA SER ALA ASP VAL GLU LYS MET SEQRES 10 A 181 ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP LYS ARG GLN SEQRES 11 A 181 VAL SER LYS GLU ARG GLY GLU LYS LEU ALA LEU ASP TYR SEQRES 12 A 181 GLY ILE LYS PHE MET GLU THR SER ALA LYS ALA ASN ILE SEQRES 13 A 181 ASN VAL GLU ASN ALA PHE PHE THR LEU ALA ARG ASP ILE SEQRES 14 A 181 LYS ALA LYS MET ASP LYS LYS LEU GLU GLY ASN SER SEQRES 1 C 38 ARG ALA GLU ALA GLU GLN GLU LYS ASP GLN LEU ARG THR SEQRES 2 C 38 GLN VAL VAL ARG LEU GLN ALA GLU LYS ALA ASP LEU LEU SEQRES 3 C 38 GLY ILE VAL SER GLU LEU GLN LEU LYS LEU ASN SER SEQRES 1 D 38 ARG ALA GLU ALA GLU GLN GLU LYS ASP GLN LEU ARG THR SEQRES 2 D 38 GLN VAL VAL ARG LEU GLN ALA GLU LYS ALA ASP LEU LEU SEQRES 3 D 38 GLY ILE VAL SER GLU LEU GLN LEU LYS LEU ASN SER SEQRES 1 B 181 MET ALA LYS THR TYR ASP TYR LEU PHE LYS LEU LEU LEU SEQRES 2 B 181 ILE GLY ASP SER GLY VAL GLY LYS THR CYS VAL LEU PHE SEQRES 3 B 181 ARG PHE SER GLU ASP ALA PHE ASN SER THR PHE ILE SER SEQRES 4 B 181 THR ILE GLY ILE ASP PHE LYS ILE ARG THR ILE GLU LEU SEQRES 5 B 181 ASP GLY LYS ARG ILE LYS LEU GLN ILE TRP ASP THR ALA SEQRES 6 B 181 GLY LEU GLU ARG PHE ARG THR ILE THR THR ALA TYR TYR SEQRES 7 B 181 ARG GLY ALA MET GLY ILE MET LEU VAL TYR ASP ILE THR SEQRES 8 B 181 ASN GLU LYS SER PHE ASP ASN ILE ARG ASN TRP ILE ARG SEQRES 9 B 181 ASN ILE GLU GLU HIS ALA SER ALA ASP VAL GLU LYS MET SEQRES 10 B 181 ILE LEU GLY ASN LYS CYS ASP VAL ASN ASP LYS ARG GLN SEQRES 11 B 181 VAL SER LYS GLU ARG GLY GLU LYS LEU ALA LEU ASP TYR SEQRES 12 B 181 GLY ILE LYS PHE MET GLU THR SER ALA LYS ALA ASN ILE SEQRES 13 B 181 ASN VAL GLU ASN ALA PHE PHE THR LEU ALA ARG ASP ILE SEQRES 14 B 181 LYS ALA LYS MET ASP LYS LYS LEU GLU GLY ASN SER HET GTP A 201 32 HET MG A 202 1 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET EDO A 207 4 HET GTP B 201 32 HET GOL B 202 6 HET GOL B 203 6 HET GOL B 204 6 HET GOL B 205 6 HET MG B 206 1 HET EDO B 207 4 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GTP 2(C10 H16 N5 O14 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 EDO 6(C2 H6 O2) FORMUL 13 GOL 4(C3 H8 O3) FORMUL 19 HOH *407(H2 O) HELIX 1 AA1 GLY A 20 ASP A 31 1 12 HELIX 2 AA2 LEU A 67 ARG A 69 5 3 HELIX 3 AA3 PHE A 70 ALA A 76 1 7 HELIX 4 AA4 ASN A 92 ASN A 98 1 7 HELIX 5 AA5 ASN A 98 ALA A 110 1 13 HELIX 6 AA6 VAL A 125 ARG A 129 5 5 HELIX 7 AA7 SER A 132 TYR A 143 1 12 HELIX 8 AA8 ASN A 157 LYS A 176 1 20 HELIX 9 AA9 GLU C 139 ASN C 169 1 31 HELIX 10 AB1 GLU D 139 ASN D 169 1 31 HELIX 11 AB2 GLY B 20 ASP B 31 1 12 HELIX 12 AB3 LEU B 67 ARG B 69 5 3 HELIX 13 AB4 PHE B 70 ALA B 76 1 7 HELIX 14 AB5 ASN B 92 ASN B 98 1 7 HELIX 15 AB6 ASN B 98 ALA B 110 1 13 HELIX 16 AB7 SER B 132 TYR B 143 1 12 HELIX 17 AB8 ASN B 157 GLY B 179 1 23 SHEET 1 AA1 6 ILE A 43 LEU A 52 0 SHEET 2 AA1 6 LYS A 55 THR A 64 -1 O ILE A 57 N ILE A 50 SHEET 3 AA1 6 TYR A 7 ILE A 14 1 N LEU A 11 O TRP A 62 SHEET 4 AA1 6 GLY A 83 ASP A 89 1 O MET A 85 N ILE A 14 SHEET 5 AA1 6 GLU A 115 ASN A 121 1 O MET A 117 N LEU A 86 SHEET 6 AA1 6 LYS A 146 GLU A 149 1 O LYS A 146 N ILE A 118 SHEET 1 AA2 6 ILE B 43 LEU B 52 0 SHEET 2 AA2 6 LYS B 55 THR B 64 -1 O ILE B 57 N ILE B 50 SHEET 3 AA2 6 TYR B 7 GLY B 15 1 N LEU B 11 O TRP B 62 SHEET 4 AA2 6 GLY B 83 ASP B 89 1 O MET B 85 N LEU B 12 SHEET 5 AA2 6 GLU B 115 ASN B 121 1 O MET B 117 N LEU B 86 SHEET 6 AA2 6 LYS B 146 GLU B 149 1 O LYS B 146 N ILE B 118 LINK OG1 THR A 22 MG MG A 202 1555 1555 2.06 LINK OG1 THR A 40 MG MG A 202 1555 1555 2.10 LINK O1G GTP A 201 MG MG A 202 1555 1555 1.99 LINK O2B GTP A 201 MG MG A 202 1555 1555 2.05 LINK MG MG A 202 O HOH A 303 1555 1555 2.12 LINK MG MG A 202 O HOH A 321 1555 1555 2.10 LINK OG1 THR B 22 MG MG B 206 1555 1555 2.07 LINK OG1 THR B 40 MG MG B 206 1555 1555 2.16 LINK O1G GTP B 201 MG MG B 206 1555 1555 2.06 LINK O2B GTP B 201 MG MG B 206 1555 1555 2.10 LINK MG MG B 206 O HOH B 321 1555 1555 2.13 LINK MG MG B 206 O HOH B 347 1555 1555 2.09 CRYST1 67.218 69.432 110.337 90.00 90.00 90.00 P 21 21 21 8 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 0.014877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014403 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009063 0.00000