HEADER MOTOR PROTEIN/STRUCTURAL PROTEIN 19-JUL-19 6KIQ TITLE COMPLEX OF YEAST CYTOPLASMIC DYNEIN MTBD-HIGH AND MT WITH DTT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA TUBULIN; COMPND 3 CHAIN: a; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: TUBULIN BETA CHAIN; COMPND 6 CHAIN: b; COMPND 7 SYNONYM: BETA-TUBULIN; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: DYNEIN HEAVY CHAIN, CYTOPLASMIC; COMPND 10 CHAIN: M; COMPND 11 SYNONYM: DYNEIN HEAVY CHAIN,CYTOSOLIC,DYHC; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_TAXID: 9823; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 6 ORGANISM_COMMON: PIG; SOURCE 7 ORGANISM_TAXID: 9823; SOURCE 8 MOL_ID: 3; SOURCE 9 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 10 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 11 ORGANISM_TAXID: 559292; SOURCE 12 STRAIN: S288C; SOURCE 13 GENE: DYN1, DHC1, YKR054C; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DYNEIN, MICROTUBULE, MOTOR PROTEIN-STRUCTURAL PROTEIN COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR Y.KOMORI,N.NISHIDA,I.SHIMADA,M.KIKKAWA REVDAT 3 27-MAR-24 6KIQ 1 REMARK REVDAT 2 11-MAR-20 6KIQ 1 JRNL REVDAT 1 04-MAR-20 6KIQ 0 JRNL AUTH N.NISHIDA,Y.KOMORI,O.TAKARADA,A.WATANABE,S.TAMURA,S.KUBO, JRNL AUTH 2 I.SHIMADA,M.KIKKAWA JRNL TITL STRUCTURAL BASIS FOR TWO-WAY COMMUNICATION BETWEEN DYNEIN JRNL TITL 2 AND MICROTUBULES. JRNL REF NAT COMMUN V. 11 1038 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32098965 JRNL DOI 10.1038/S41467-020-14842-8 REMARK 2 REMARK 2 RESOLUTION. 3.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GCTF, MDFF, RELION, FREALIGN REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.620 REMARK 3 NUMBER OF PARTICLES : 32666 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: FSCTRUE WAS CALCULATED TO VALIDATE THE RESOLUTION. REMARK 4 REMARK 4 6KIQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300013005. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : MTBD-HIGH/MT COMPLEX WITH DTT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 6.80 REMARK 245 SAMPLE DETAILS : DTT WAS ADDED TO CLEAVE THE REMARK 245 DISULFIDE BOND BETWEEN CC1 AND CC2 OF MTBD-HIGH REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 621 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5400.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: a, b, M 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 HH22 ARG b 243 OD2 ASP b 251 1.50 REMARK 500 OE2 GLU b 200 HH TYR b 202 1.50 REMARK 500 HG1 THR b 287 OE2 GLU b 290 1.52 REMARK 500 OD2 ASP b 69 HG1 THR b 74 1.53 REMARK 500 HG SER a 1152 OE2 GLU a 1157 1.55 REMARK 500 O GLU a 1228 H ASN a 1232 1.56 REMARK 500 OD1 ASN a 1232 HZ2 LYS a 1326 1.56 REMARK 500 OE1 GLU b 71 H GLY b 73 1.56 REMARK 500 OD2 ASP a 1072 HH22 ARG a 1079 1.56 REMARK 500 HG SER b 97 OE1 GLU b 110 1.57 REMARK 500 HG SER b 126 OE2 GLU b 127 1.57 REMARK 500 O THR b 74 HG SER b 77 1.57 REMARK 500 O PRO a 1149 HZ1 LYS a 1368 1.57 REMARK 500 OE1 GLU a 1027 HG SER a 1210 1.57 REMARK 500 O TYR b 210 H CYS b 213 1.58 REMARK 500 OD1 ASP b 163 HE ARG b 164 1.59 REMARK 500 HH TYR a 1082 OE2 GLU a 1391 1.59 REMARK 500 HZ3 LYS a 1070 OE2 GLU a 1071 1.59 REMARK 500 O VAL a 1302 H ALA a 1304 1.59 REMARK 500 O ASP a 1370 H ALA a 1374 1.60 REMARK 500 O LEU a 1204 H GLN a 1207 1.60 REMARK 500 O VAL b 182 H TYR b 185 1.60 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 VAL a1014 CA VAL a1014 CB -0.127 REMARK 500 TYR a1024 CA TYR a1024 C -0.161 REMARK 500 GLU a1045 C PRO a1046 N -0.121 REMARK 500 PHE a1112 CB PHE a1112 CG -0.105 REMARK 500 GLY a1120 CA GLY a1120 C -0.098 REMARK 500 PRO a1235 CA PRO a1235 C -0.130 REMARK 500 PHE a1241 C PRO a1242 N -0.137 REMARK 500 PRO a1248 CD PRO a1248 N -0.090 REMARK 500 VAL a1262 CA VAL a1262 CB -0.132 REMARK 500 CYS a1289 CB CYS a1289 SG -0.099 REMARK 500 GLY a1328 CA GLY a1328 C -0.104 REMARK 500 CYS a1350 CB CYS a1350 SG -0.128 REMARK 500 TYR a1406 CB TYR a1406 CG -0.092 REMARK 500 HIS b 6 CB HIS b 6 CG -0.111 REMARK 500 GLY b 17 CA GLY b 17 C -0.107 REMARK 500 TRP b 21 NE1 TRP b 21 CE2 -0.104 REMARK 500 PRO b 63 CA PRO b 63 C -0.149 REMARK 500 MET b 269 C PRO b 270 N -0.159 REMARK 500 ALA b 273 C PRO b 274 N -0.126 REMARK 500 PRO b 274 CD PRO b 274 N -0.089 REMARK 500 TYR b 432 CB TYR b 432 CG -0.093 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 ARG a1002 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 GLN a1011 N - CA - CB ANGL. DEV. = 12.0 DEGREES REMARK 500 CYS a1020 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 VAL a1040 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 VAL a1042 CA - CB - CG2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG a1053 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 TYR a1057 N - CA - CB ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG a1058 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ASP a1072 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG a1079 N - CA - CB ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG a1079 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG a1079 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR a1082 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG a1095 N - CA - CB ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG a1095 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG a1095 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG a1130 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 PHE a1143 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE a1143 CB - CG - CD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 TYR a1159 CB - CG - CD2 ANGL. DEV. = 3.6 DEGREES REMARK 500 CYS a1174 CB - CA - C ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG a1189 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG a1195 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 TYR a1198 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR a1198 CB - CG - CD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG a1203 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG a1203 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ALA a1214 N - CA - CB ANGL. DEV. = 12.9 DEGREES REMARK 500 SER a1215 CB - CA - C ANGL. DEV. = -15.2 DEGREES REMARK 500 SER a1215 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG a1217 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG a1217 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PHE a1218 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 LEU a1222 N - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 PHE a1229 CB - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 PHE a1229 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 THR a1231 CA - CB - CG2 ANGL. DEV. = -11.2 DEGREES REMARK 500 PRO a1235 C - N - CD ANGL. DEV. = -17.6 DEGREES REMARK 500 ALA a1247 CA - C - N ANGL. DEV. = 21.0 DEGREES REMARK 500 CYS a1269 CA - CB - SG ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG a1282 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG a1282 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 CYS a1289 CA - CB - SG ANGL. DEV. = -11.6 DEGREES REMARK 500 CYS a1290 O - C - N ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG a1294 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 PRO a1299 C - N - CA ANGL. DEV. = 9.9 DEGREES REMARK 500 LYS a1300 N - CA - CB ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG a1313 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 PRO a1322 C - N - CD ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG a1347 CB - CA - C ANGL. DEV. = -13.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 122 ANGLE DEVIATIONS. 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 TYR a1024 -74.43 -51.91 REMARK 500 GLN a1031 -150.14 -71.22 REMARK 500 PRO a1032 40.08 -88.10 REMARK 500 ASP a1033 136.60 172.28 REMARK 500 LEU a1044 32.08 -94.50 REMARK 500 GLU a1045 106.86 -164.26 REMARK 500 TYR a1057 34.31 100.80 REMARK 500 LEU a1060 43.89 -98.73 REMARK 500 LYS a1070 -7.49 -154.05 REMARK 500 GLU a1071 -150.76 -80.98 REMARK 500 ALA a1074 -160.71 54.37 REMARK 500 ASN a1075 38.79 -164.93 REMARK 500 TYR a1077 -77.58 -36.77 REMARK 500 ALA a1078 -66.99 -21.79 REMARK 500 TYR a1082 -115.65 -71.75 REMARK 500 THR a1083 -92.04 -0.73 REMARK 500 ILE a1084 -70.61 -69.19 REMARK 500 ASP a1090 -71.64 -41.98 REMARK 500 SER a1121 -70.82 -83.19 REMARK 500 PHE a1123 -70.68 -25.02 REMARK 500 SER a1132 -18.23 -47.79 REMARK 500 TYR a1135 43.91 -144.46 REMARK 500 LYS a1138 -176.54 -66.48 REMARK 500 ALA a1148 157.35 -24.24 REMARK 500 VAL a1151 35.30 -68.39 REMARK 500 HIS a1171 -0.82 -170.07 REMARK 500 ALA a1182 -7.99 -56.21 REMARK 500 LEU a1191 -45.37 -177.35 REMARK 500 ASP a1192 70.84 79.73 REMARK 500 ARG a1195 58.24 -105.43 REMARK 500 ILE a1212 -83.81 -71.27 REMARK 500 THR a1213 -86.96 -66.53 REMARK 500 ALA a1214 -75.89 -6.99 REMARK 500 ARG a1217 1.49 -61.79 REMARK 500 ASP a1219 111.86 59.46 REMARK 500 ALA a1221 -11.83 -168.16 REMARK 500 LEU a1222 95.45 179.70 REMARK 500 GLU a1228 -51.82 -27.72 REMARK 500 PHE a1229 -81.36 -45.66 REMARK 500 GLN a1230 -34.44 -29.31 REMARK 500 PRO a1235 26.56 -154.96 REMARK 500 TYR a1236 -153.08 -168.29 REMARK 500 HIS a1240 150.09 -5.21 REMARK 500 PRO a1242 174.15 -58.08 REMARK 500 ALA a1247 -94.35 -116.12 REMARK 500 GLU a1253 26.50 -144.28 REMARK 500 HIS a1257 59.76 -159.47 REMARK 500 GLU a1258 -179.57 45.18 REMARK 500 ALA a1263 -26.45 -34.14 REMARK 500 PRO a1272 25.05 -77.23 REMARK 500 REMARK 500 THIS ENTRY HAS 173 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG a 1002 GLU a 1003 -147.38 REMARK 500 GLU a 1003 CYS a 1004 -139.94 REMARK 500 PRO a 1037 ARG a 1038 -145.67 REMARK 500 GLN a 1059 LEU a 1060 -141.38 REMARK 500 ALA a 1074 ASN a 1075 137.34 REMARK 500 THR a 1119 GLY a 1120 -98.21 REMARK 500 GLY a 1120 SER a 1121 148.27 REMARK 500 ILE a 1145 TYR a 1146 -143.41 REMARK 500 GLN a 1230 THR a 1231 142.33 REMARK 500 HIS a 1240 PHE a 1241 -148.19 REMARK 500 PRO a 1242 LEU a 1243 144.99 REMARK 500 ALA a 1247 PRO a 1248 -149.73 REMARK 500 GLU a 1253 LYS a 1254 144.30 REMARK 500 THR a 1323 GLY a 1324 134.88 REMARK 500 THR a 1335 VAL a 1336 -148.62 REMARK 500 GLY a 1410 VAL a 1411 144.26 REMARK 500 ILE b 4 VAL b 5 -149.96 REMARK 500 GLY b 100 ASN b 101 -131.46 REMARK 500 HIS b 107 TYR b 108 146.76 REMARK 500 CYS b 129 ASP b 130 144.67 REMARK 500 ASP b 179 THR b 180 147.50 REMARK 500 THR b 216 LEU b 217 141.35 REMARK 500 MET b 259 VAL b 260 -144.79 REMARK 500 ILE b 347 PRO b 348 -146.76 REMARK 500 LYS b 402 ALA b 403 -133.61 REMARK 500 PHE b 404 LEU b 405 -141.78 REMARK 500 GLU b 415 MET b 416 -147.40 REMARK 500 SER M 3203 LYS M 3204 143.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 HIS a1008 0.11 SIDE CHAIN REMARK 500 TYR a1024 0.24 SIDE CHAIN REMARK 500 ARG a1038 0.15 SIDE CHAIN REMARK 500 PHE a1041 0.08 SIDE CHAIN REMARK 500 TYR a1057 0.11 SIDE CHAIN REMARK 500 ARG a1058 0.13 SIDE CHAIN REMARK 500 ARG a1079 0.19 SIDE CHAIN REMARK 500 TYR a1082 0.12 SIDE CHAIN REMARK 500 ARG a1097 0.10 SIDE CHAIN REMARK 500 PHE a1112 0.13 SIDE CHAIN REMARK 500 PHE a1123 0.08 SIDE CHAIN REMARK 500 TYR a1135 0.08 SIDE CHAIN REMARK 500 TYR a1184 0.10 SIDE CHAIN REMARK 500 ARG a1195 0.08 SIDE CHAIN REMARK 500 TYR a1198 0.13 SIDE CHAIN REMARK 500 ARG a1203 0.12 SIDE CHAIN REMARK 500 ARG a1217 0.15 SIDE CHAIN REMARK 500 PHE a1229 0.11 SIDE CHAIN REMARK 500 TYR a1236 0.08 SIDE CHAIN REMARK 500 ARG a1238 0.15 SIDE CHAIN REMARK 500 TYR a1246 0.09 SIDE CHAIN REMARK 500 TYR a1256 0.08 SIDE CHAIN REMARK 500 ARG a1294 0.17 SIDE CHAIN REMARK 500 ARG a1313 0.17 SIDE CHAIN REMARK 500 ARG a1364 0.08 SIDE CHAIN REMARK 500 PHE a1378 0.10 SIDE CHAIN REMARK 500 ARG a1396 0.11 SIDE CHAIN REMARK 500 TYR a1406 0.09 SIDE CHAIN REMARK 500 ARG b 2 0.12 SIDE CHAIN REMARK 500 HIS b 28 0.08 SIDE CHAIN REMARK 500 HIS b 37 0.09 SIDE CHAIN REMARK 500 ARG b 64 0.10 SIDE CHAIN REMARK 500 ARG b 79 0.13 SIDE CHAIN REMARK 500 PHE b 92 0.09 SIDE CHAIN REMARK 500 TYR b 161 0.07 SIDE CHAIN REMARK 500 TYR b 185 0.09 SIDE CHAIN REMARK 500 TYR b 210 0.16 SIDE CHAIN REMARK 500 ARG b 215 0.09 SIDE CHAIN REMARK 500 ARG b 311 0.20 SIDE CHAIN REMARK 500 TYR b 312 0.19 SIDE CHAIN REMARK 500 PHE b 388 0.09 SIDE CHAIN REMARK 500 ARG b 390 0.09 SIDE CHAIN REMARK 500 PHE b 395 0.10 SIDE CHAIN REMARK 500 ARG b 400 0.11 SIDE CHAIN REMARK 500 PHE b 404 0.12 SIDE CHAIN REMARK 500 TYR b 408 0.09 SIDE CHAIN REMARK 500 PHE b 418 0.08 SIDE CHAIN REMARK 500 TYR b 432 0.17 SIDE CHAIN REMARK 500 TYR b 435 0.11 SIDE CHAIN REMARK 500 ARG M3110 0.11 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 52 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER a1161 -11.01 REMARK 500 ALA a1244 13.13 REMARK 500 MET b 416 -10.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-9996 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-9997 RELATED DB: EMDB REMARK 900 COMPLEX OF YEAST CYTOPLASMIC DYNEIN MTBD-HIGH AND MT WITH DTT DBREF 6KIQ a 1002 1413 PDB 6KIQ 6KIQ 1002 1413 DBREF 6KIQ b 2 437 UNP P02554 TBB_PIG 2 427 DBREF 6KIQ M 3095 3224 UNP P36022 DYHC_YEAST 3095 3224 SEQADV 6KIQ CYS M 3101 UNP P36022 ILE 3101 ENGINEERED MUTATION SEQADV 6KIQ CYS M 3222 UNP P36022 VAL 3222 ENGINEERED MUTATION SEQRES 1 a 412 ARG GLU CYS ILE SER ILE HIS VAL GLY GLN ALA GLY VAL SEQRES 2 a 412 GLN ILE GLY ASN ALA CYS TRP GLU LEU TYR CYS LEU GLU SEQRES 3 a 412 HIS GLY ILE GLN PRO ASP GLY HIS VAL PRO ARG ALA VAL SEQRES 4 a 412 PHE VAL ASP LEU GLU PRO THR VAL ILE ASP GLU VAL ARG SEQRES 5 a 412 THR GLY THR TYR ARG GLN LEU PHE HIS PRO GLU GLN LEU SEQRES 6 a 412 ILE THR GLY LYS GLU ASP ALA ALA ASN ASN TYR ALA ARG SEQRES 7 a 412 GLY HIS TYR THR ILE GLY LYS GLU ILE ILE ASP LEU VAL SEQRES 8 a 412 LEU ASP ARG ILE ARG LYS LEU ALA ASP GLN CYS THR GLY SEQRES 9 a 412 LEU GLN GLY PHE SER VAL PHE HIS SER PHE GLY GLY GLY SEQRES 10 a 412 THR GLY SER GLY PHE THR SER LEU LEU MET GLU ARG LEU SEQRES 11 a 412 SER VAL ASP TYR GLY LYS LYS SER LYS LEU GLU PHE SER SEQRES 12 a 412 ILE TYR PRO ALA PRO GLN VAL SER THR ALA VAL VAL GLU SEQRES 13 a 412 PRO TYR ASN SER ILE LEU THR THR HIS THR THR LEU GLU SEQRES 14 a 412 HIS SER ASP CYS ALA PHE MET VAL ASP ASN GLU ALA ILE SEQRES 15 a 412 TYR ASP ILE CYS ARG ARG ASN LEU ASP ILE GLU ARG PRO SEQRES 16 a 412 THR TYR THR ASN LEU ASN ARG LEU ILE GLY GLN ILE VAL SEQRES 17 a 412 SER SER ILE THR ALA SER LEU ARG PHE ASP GLY ALA LEU SEQRES 18 a 412 ASN VAL ASP LEU THR GLU PHE GLN THR ASN LEU VAL PRO SEQRES 19 a 412 TYR PRO ARG GLY HIS PHE PRO LEU ALA THR TYR ALA PRO SEQRES 20 a 412 VAL ILE SER ALA GLU LYS ALA TYR HIS GLU GLN LEU SER SEQRES 21 a 412 VAL ALA GLU ILE THR ASN ALA CYS PHE GLU PRO ALA ASN SEQRES 22 a 412 GLN MET VAL LYS CYS ASP PRO ARG HIS GLY LYS TYR MET SEQRES 23 a 412 ALA CYS CYS LEU LEU TYR ARG GLY ASP VAL VAL PRO LYS SEQRES 24 a 412 ASP VAL ASN ALA ALA ILE ALA THR ILE LYS THR LYS ARG SEQRES 25 a 412 THR ILE GLN PHE VAL ASP TRP CYS PRO THR GLY PHE LYS SEQRES 26 a 412 VAL GLY ILE ASN TYR GLU PRO PRO THR VAL VAL PRO GLY SEQRES 27 a 412 GLY ASP LEU ALA LYS VAL GLN ARG ALA VAL CYS MET LEU SEQRES 28 a 412 SER ASN THR THR ALA ILE ALA GLU ALA TRP ALA ARG LEU SEQRES 29 a 412 ASP HIS LYS PHE ASP LEU MET TYR ALA LYS ARG ALA PHE SEQRES 30 a 412 VAL HIS TRP TYR VAL GLY GLU GLY MET GLU GLU GLY GLU SEQRES 31 a 412 PHE SER GLU ALA ARG GLU ASP MET ALA ALA LEU GLU LYS SEQRES 32 a 412 ASP TYR GLU GLU VAL GLY VAL ASP SER SEQRES 1 b 426 ARG GLU ILE VAL HIS ILE GLN ALA GLY GLN CYS GLY ASN SEQRES 2 b 426 GLN ILE GLY ALA LYS PHE TRP GLU VAL ILE SER ASP GLU SEQRES 3 b 426 HIS GLY ILE ASP PRO THR GLY SER TYR HIS GLY ASP SER SEQRES 4 b 426 ASP LEU GLN LEU GLU ARG ILE ASN VAL TYR TYR ASN GLU SEQRES 5 b 426 ALA ALA GLY ASN LYS TYR VAL PRO ARG ALA ILE LEU VAL SEQRES 6 b 426 ASP LEU GLU PRO GLY THR MET ASP SER VAL ARG SER GLY SEQRES 7 b 426 PRO PHE GLY GLN ILE PHE ARG PRO ASP ASN PHE VAL PHE SEQRES 8 b 426 GLY GLN SER GLY ALA GLY ASN ASN TRP ALA LYS GLY HIS SEQRES 9 b 426 TYR THR GLU GLY ALA GLU LEU VAL ASP SER VAL LEU ASP SEQRES 10 b 426 VAL VAL ARG LYS GLU SER GLU SER CYS ASP CYS LEU GLN SEQRES 11 b 426 GLY PHE GLN LEU THR HIS SER LEU GLY GLY GLY THR GLY SEQRES 12 b 426 SER GLY MET GLY THR LEU LEU ILE SER LYS ILE ARG GLU SEQRES 13 b 426 GLU TYR PRO ASP ARG ILE MET ASN THR PHE SER VAL VAL SEQRES 14 b 426 PRO SER PRO LYS VAL SER ASP THR VAL VAL GLU PRO TYR SEQRES 15 b 426 ASN ALA THR LEU SER VAL HIS GLN LEU VAL GLU ASN THR SEQRES 16 b 426 ASP GLU THR TYR CYS ILE ASP ASN GLU ALA LEU TYR ASP SEQRES 17 b 426 ILE CYS PHE ARG THR LEU LYS LEU THR THR PRO THR TYR SEQRES 18 b 426 GLY ASP LEU ASN HIS LEU VAL SER ALA THR MET SER GLY SEQRES 19 b 426 VAL THR THR CYS LEU ARG PHE PRO GLY GLN LEU ASN ALA SEQRES 20 b 426 ASP LEU ARG LYS LEU ALA VAL ASN MET VAL PRO PHE PRO SEQRES 21 b 426 ARG LEU HIS PHE PHE MET PRO GLY PHE ALA PRO LEU THR SEQRES 22 b 426 SER ARG GLY SER GLN GLN TYR ARG ALA LEU THR VAL PRO SEQRES 23 b 426 GLU LEU THR GLN GLN MET PHE ASP ALA LYS ASN MET MET SEQRES 24 b 426 ALA ALA CYS ASP PRO ARG HIS GLY ARG TYR LEU THR VAL SEQRES 25 b 426 ALA ALA VAL PHE ARG GLY ARG MET SER MET LYS GLU VAL SEQRES 26 b 426 ASP GLU GLN MET LEU ASN VAL GLN ASN LYS ASN SER SER SEQRES 27 b 426 TYR PHE VAL GLU TRP ILE PRO ASN ASN VAL LYS THR ALA SEQRES 28 b 426 VAL CYS ASP ILE PRO PRO ARG GLY LEU LYS MET SER ALA SEQRES 29 b 426 THR PHE ILE GLY ASN SER THR ALA ILE GLN GLU LEU PHE SEQRES 30 b 426 LYS ARG ILE SER GLU GLN PHE THR ALA MET PHE ARG ARG SEQRES 31 b 426 LYS ALA PHE LEU HIS TRP TYR THR GLY GLU GLY MET ASP SEQRES 32 b 426 GLU MET GLU PHE THR GLU ALA GLU SER ASN MET ASN ASP SEQRES 33 b 426 LEU VAL SER GLU TYR GLN GLN TYR GLN ASP SEQRES 1 M 130 MET LYS SER ILE GLN ASP CYS GLU PRO THR ILE LEU GLU SEQRES 2 M 130 ALA GLN ARG GLY VAL LYS ASN ILE LYS LYS GLN GLN LEU SEQRES 3 M 130 THR GLU ILE ARG SER MET VAL ASN PRO PRO SER GLY VAL SEQRES 4 M 130 LYS ILE VAL MET GLU ALA VAL CYS ALA ILE LEU GLY TYR SEQRES 5 M 130 GLN PHE SER ASN TRP ARG ASP ILE GLN GLN PHE ILE ARG SEQRES 6 M 130 LYS ASP ASP PHE ILE HIS ASN ILE VAL HIS TYR ASP THR SEQRES 7 M 130 THR LEU HIS MET LYS PRO GLN ILE ARG LYS TYR MET GLU SEQRES 8 M 130 GLU GLU PHE LEU SER ASP PRO ASN PHE THR TYR GLU THR SEQRES 9 M 130 ILE ASN ARG ALA SER LYS ALA CYS GLY PRO LEU TYR GLN SEQRES 10 M 130 TRP VAL ASN ALA GLN ILE ASN PHE SER LYS CYS LEU GLU HELIX 1 AA1 GLY a 1010 GLY a 1029 1 20 HELIX 2 AA2 PRO a 1046 GLY a 1055 1 10 HELIX 3 AA3 HIS a 1062 GLU a 1064 5 3 HELIX 4 AA4 ASN a 1076 TYR a 1082 1 7 HELIX 5 AA5 TYR a 1082 ASP a 1101 1 20 HELIX 6 AA6 SER a 1121 TYR a 1135 1 15 HELIX 7 AA7 VAL a 1156 GLU a 1170 1 15 HELIX 8 AA8 ASP a 1179 ASN a 1190 1 12 HELIX 9 AA9 THR a 1197 ARG a 1217 1 21 HELIX 10 AB1 ASP a 1225 LEU a 1233 1 9 HELIX 11 AB2 SER a 1261 GLU a 1271 1 11 HELIX 12 AB3 ASP a 1280 GLY a 1284 5 5 HELIX 13 AB4 VAL a 1298 THR a 1311 1 14 HELIX 14 AB5 ILE a 1358 ARG a 1376 1 19 HELIX 15 AB6 VAL a 1379 GLY a 1384 1 6 HELIX 16 AB7 GLU a 1388 LYS a 1404 1 17 HELIX 17 AB8 LYS a 1404 VAL a 1409 1 6 HELIX 18 AB9 GLY b 10 GLU b 27 1 18 HELIX 19 AC1 SER b 40 GLU b 47 1 6 HELIX 20 AC2 ARG b 48 TYR b 52 5 5 HELIX 21 AC3 THR b 74 ARG b 79 1 6 HELIX 22 AC4 ARG b 88 ASP b 90 5 3 HELIX 23 AC5 TRP b 103 HIS b 107 5 5 HELIX 24 AC6 GLU b 110 VAL b 115 1 6 HELIX 25 AC7 VAL b 115 GLU b 127 1 13 HELIX 26 AC8 GLY b 143 GLY b 148 1 6 HELIX 27 AC9 GLY b 148 TYR b 161 1 14 HELIX 28 AD1 VAL b 182 VAL b 195 1 14 HELIX 29 AD2 ASP b 205 ARG b 215 1 11 HELIX 30 AD3 THR b 223 VAL b 238 1 16 HELIX 31 AD4 THR b 239 PHE b 244 5 6 HELIX 32 AD5 ASP b 251 ASN b 258 1 8 HELIX 33 AD6 SER b 277 GLN b 281 5 5 HELIX 34 AD7 VAL b 288 PHE b 296 1 9 HELIX 35 AD8 ASP b 306 GLY b 310 5 5 HELIX 36 AD9 SER b 324 ASN b 339 1 16 HELIX 37 AE1 SER b 340 PHE b 343 5 4 HELIX 38 AE2 SER b 381 ALA b 383 5 3 HELIX 39 AE3 ILE b 384 ARG b 400 1 17 HELIX 40 AE4 LEU b 405 GLY b 410 1 6 HELIX 41 AE5 GLU b 415 TYR b 435 1 21 HELIX 42 AE6 PRO M 3103 ASN M 3114 1 12 HELIX 43 AE7 LYS M 3116 MET M 3126 1 11 HELIX 44 AE8 PRO M 3130 GLY M 3145 1 16 HELIX 45 AE9 ASN M 3150 ARG M 3159 1 10 HELIX 46 AF1 ASP M 3161 TYR M 3170 1 10 HELIX 47 AF2 GLN M 3179 LEU M 3189 1 11 HELIX 48 AF3 THR M 3195 SER M 3203 1 9 HELIX 49 AF4 ALA M 3205 PHE M 3219 1 15 SHEET 1 AA1 6 LEU a1066 THR a1068 0 SHEET 2 AA1 6 VAL a1040 ASP a1043 1 N PHE a1041 O ILE a1067 SHEET 3 AA1 6 SER a1006 VAL a1009 1 N SER a1006 O VAL a1040 SHEET 4 AA1 6 GLY a1108 VAL a1111 1 O SER a1110 N ILE a1007 SHEET 5 AA1 6 SER a1139 ILE a1145 1 O SER a1139 N PHE a1109 SHEET 6 AA1 6 CYS a1174 VAL a1178 1 O PHE a1176 N SER a1144 SHEET 1 AA2 3 PRO a1242 LEU a1243 0 SHEET 2 AA2 3 SER a1353 THR a1355 -1 O SER a1353 N LEU a1243 SHEET 3 AA2 3 TYR a1286 CYS a1289 -1 N MET a1287 O ASN a1354 SHEET 1 AA3 3 GLY a1328 ASN a1330 0 SHEET 2 AA3 3 LEU a1292 GLY a1295 1 N TYR a1293 O GLY a1328 SHEET 3 AA3 3 ARG a1347 CYS a1350 -1 O CYS a1350 N LEU a1292 SHEET 1 AA410 PHE b 92 PHE b 94 0 SHEET 2 AA410 LEU b 67 ASP b 69 1 N LEU b 67 O VAL b 93 SHEET 3 AA410 GLU b 3 ALA b 9 1 N GLN b 8 O VAL b 68 SHEET 4 AA410 LEU b 132 HIS b 139 1 O GLN b 133 N GLU b 3 SHEET 5 AA410 ILE b 165 SER b 170 1 O ASN b 167 N LEU b 137 SHEET 6 AA410 GLU b 200 TYR b 202 1 O TYR b 202 N THR b 168 SHEET 7 AA410 PHE b 267 GLY b 271 1 O PHE b 268 N THR b 201 SHEET 8 AA410 ALA b 375 GLY b 379 -1 O PHE b 377 N GLY b 271 SHEET 9 AA410 VAL b 318 PHE b 319 -1 N VAL b 318 O THR b 376 SHEET 10 AA410 ALA b 354 VAL b 355 1 N ALA b 354 O PHE b 319 SHEET 1 AA5 2 GLU b 55 ALA b 56 0 SHEET 2 AA5 2 LYS b 60 TYR b 61 -1 O LYS b 60 N ALA b 56 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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