HEADER MOTOR PROTEIN/STRUCTURAL PROTEIN 25-JUN-12 3J1U TITLE LOW AFFINITY DYNEIN MICROTUBULE BINDING DOMAIN - TUBULIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOPLASMIC DYNEIN 1 HEAVY CHAIN 1, SERYL T-RNA SYNTHETASE COMPND 3 CHIMERA; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SEE REMARK 999; COMPND 6 SYNONYM: CYTOPLASMIC DYNEIN HEAVY CHAIN 1, DYNEIN HEAVY CHAIN, COMPND 7 CYTOSOLIC; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TUBULIN ALPHA-1B CHAIN; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: ALPHA-TUBULIN UBIQUITOUS, TUBULIN K-ALPHA-1, TUBULIN ALPHA- COMPND 13 UBIQUITOUS CHAIN; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: TUBULIN BETA-2B CHAIN; COMPND 16 CHAIN: C; COMPND 17 SYNONYM: BETA TUBULIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DYNC1H1, DHC1, DNCH1, DNCHC1, DYHC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 10 ORGANISM_COMMON: BOVINE; SOURCE 11 ORGANISM_TAXID: 9913; SOURCE 12 MOL_ID: 3; SOURCE 13 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 14 ORGANISM_COMMON: BOVINE; SOURCE 15 ORGANISM_TAXID: 9913 KEYWDS MOTOR PROTEIN-STRUCTURAL PROTEIN COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR W.B.REDWINE,R.HERNANDEZ-LOPEZ,S.ZOU,J.HUANG,S.L.RECK-PETERSON, AUTHOR 2 A.E.LESCHZINER REVDAT 5 21-FEB-24 3J1U 1 REMARK REVDAT 4 18-JUL-18 3J1U 1 REMARK REVDAT 3 27-AUG-14 3J1U 1 REMARK REVDAT 2 03-OCT-12 3J1U 1 JRNL REVDAT 1 26-SEP-12 3J1U 0 JRNL AUTH W.B.REDWINE,R.HERNANDEZ-LOPEZ,S.ZOU,J.HUANG, JRNL AUTH 2 S.L.RECK-PETERSON,A.E.LESCHZINER JRNL TITL STRUCTURAL BASIS FOR MICROTUBULE BINDING AND RELEASE BY JRNL TITL 2 DYNEIN. JRNL REF SCIENCE V. 337 1532 2012 JRNL REFN ISSN 0036-8075 JRNL PMID 22997337 JRNL DOI 10.1126/SCIENCE.1224151 REMARK 2 REMARK 2 RESOLUTION. 9.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NAMD, UCSF CHIMERA, FREALIGN, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3ERR REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : MOLECULAR DYNAMICS FORCE FIELD REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--MOLECULAR DYNAMICS EQUILIBRATION REMARK 3 REFINEMENT PROTOCOL--RIGID BODY DETAILS--EXPLICIT SOLVENT REMARK 3 MOLECULAR DYNAMICS REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.988 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 9.700 REMARK 3 NUMBER OF PARTICLES : 10419 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV IMAGES REMARK 3 REMARK 3 OTHER DETAILS: PROJECTION MATCHING AND HELICAL SYMMETRY OPERATOR REMARK 3 DURING RECONSTRUCTION REMARK 4 REMARK 4 3J1U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000160144. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : HIGH AFFINITY CONSTRUCT OF REMARK 245 DYNEIN MICROTUBULE BINDING REMARK 245 DOMAIN BOUND TO MICROTUBULES; REMARK 245 DYNEIN MICROTUBULE BINDING REMARK 245 DOMAIN; ALPHA TUBULIN; BETA REMARK 245 TUBULIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.00 REMARK 245 SAMPLE SUPPORT DETAILS : C-FLAT 2/2-2C HOLEY CARBON REMARK 245 GRIDS (PROTOCHIPS) WERE GLOW- REMARK 245 DISCHARGED FOR 20 SECONDS AT 30 REMARK 245 MA IN AN EDWARDS CARBON REMARK 245 EVAPORATOR. REMARK 245 SAMPLE VITRIFICATION DETAILS : THE SOLUTION WAS BLOTTED REMARK 245 MANUALLY, AND THE PROCESS OF REMARK 245 ADDITION AND BLOTTING OF SRS- REMARK 245 MTBD WAS REPEATED A TOTAL OF REMARK 245 THREE TIMES. THE FINAL BLOTTING REMARK 245 WAS DONE INSIDE THE HUMIDITY REMARK 245 CHAMBER OF A VITROBOT MARK IV REMARK 245 (FEI) AT 22 CELSIUS. REMARK 245 SAMPLE BUFFER : 50 MM TRIS HCL, 1 MM MGCL2, 1MM REMARK 245 EGTA, 1MM DTT REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 10-APR-11 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 100.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.20 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 62000 REMARK 245 CALIBRATED MAGNIFICATION : 63377 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 120 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, C 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 VAL B 440 REMARK 465 GLU B 441 REMARK 465 GLY B 442 REMARK 465 GLU B 443 REMARK 465 GLY B 444 REMARK 465 GLU B 445 REMARK 465 GLU B 446 REMARK 465 GLU B 447 REMARK 465 GLY B 448 REMARK 465 GLU B 449 REMARK 465 GLU B 450 REMARK 465 TYR B 451 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A3427 O 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 TYR A3369 CD1 TYR A3369 CE1 0.099 REMARK 500 SER B 198 CA SER B 198 CB 0.098 REMARK 500 TYR B 224 CE1 TYR B 224 CZ 0.109 REMARK 500 TYR B 224 CZ TYR B 224 CE2 0.115 REMARK 500 SER B 237 CB SER B 237 OG 0.080 REMARK 500 SER B 439 C SER B 439 O -0.229 REMARK 500 TYR C 36 CG TYR C 36 CD2 0.081 REMARK 500 TYR C 185 CG TYR C 185 CD2 0.082 REMARK 500 HIS C 192 CG HIS C 192 CD2 0.056 REMARK 500 GLY C 237 CA GLY C 237 C -0.105 REMARK 500 PHE C 377 CG PHE C 377 CD1 0.099 REMARK 500 GLU C 411 CD GLU C 411 OE1 0.085 REMARK 500 ASP C 437 C ASP C 437 O -0.229 REMARK 500 ASP C 437 C ASP C 437 OXT -0.229 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 ASP A3271 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A3279 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A3279 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ALA A3290 CB - CA - C ANGL. DEV. = -10.6 DEGREES REMARK 500 ILE A3297 O - C - N ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG A3342 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 PHE A3345 CB - CG - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 TYR A3377 CB - CG - CD2 ANGL. DEV. = 3.9 DEGREES REMARK 500 TYR A3377 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR A3377 CZ - CE2 - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 TYR A3400 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 GLU A3408 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A3411 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 2 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 VAL B 14 CG1 - CB - CG2 ANGL. DEV. = -10.6 DEGREES REMARK 500 TRP B 21 CG - CD2 - CE3 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR B 24 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP B 39 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 PHE B 52 CB - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 PHE B 53 CB - CG - CD2 ANGL. DEV. = 4.7 DEGREES REMARK 500 HIS B 61 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG B 79 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 84 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 84 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 PHE B 87 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR B 108 CG - CD1 - CE1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 121 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 123 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PHE B 138 CB - CG - CD2 ANGL. DEV. = 4.9 DEGREES REMARK 500 PHE B 149 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 156 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 TYR B 161 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 TYR B 172 CB - CG - CD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 TYR B 172 CG - CD1 - CE1 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR B 185 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR B 185 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 THR B 194 N - CA - CB ANGL. DEV. = 14.1 DEGREES REMARK 500 TYR B 210 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR B 210 CB - CG - CD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 214 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 215 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 215 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ASP B 218 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP B 218 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 GLU B 220 OE1 - CD - OE2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG B 221 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 TYR B 224 CB - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR B 224 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR B 224 CD1 - CE1 - CZ ANGL. DEV. = 14.8 DEGREES REMARK 500 TYR B 224 CE1 - CZ - OH ANGL. DEV. = 20.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 140 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 PRO A3347 -39.49 -37.41 REMARK 500 SER A3384 112.38 -166.16 REMARK 500 ARG B 2 -103.07 -71.26 REMARK 500 GLU B 3 -148.23 -89.82 REMARK 500 ILE B 5 137.33 -36.25 REMARK 500 GLN B 35 107.75 73.92 REMARK 500 PRO B 37 79.36 -107.71 REMARK 500 THR B 41 125.55 72.19 REMARK 500 SER B 48 10.62 -149.24 REMARK 500 SER B 54 39.35 -92.52 REMARK 500 GLU B 55 -45.50 81.66 REMARK 500 ALA B 58 -176.50 66.09 REMARK 500 HIS B 61 124.03 61.96 REMARK 500 TYR B 83 -3.86 91.89 REMARK 500 ASP B 98 -4.28 -145.49 REMARK 500 ALA B 99 133.95 64.41 REMARK 500 ALA B 100 -11.78 -156.66 REMARK 500 TYR B 108 -63.28 -127.17 REMARK 500 GLN B 128 55.87 -113.29 REMARK 500 LEU B 132 -51.57 80.16 REMARK 500 SER B 140 67.10 83.12 REMARK 500 TYR B 161 38.77 -148.05 REMARK 500 TYR B 172 129.81 -174.90 REMARK 500 GLN B 176 -9.98 74.90 REMARK 500 ARG B 221 77.78 -113.37 REMARK 500 PHE B 244 -3.53 -178.59 REMARK 500 ASP B 245 -137.61 -92.78 REMARK 500 PRO B 263 151.93 -45.07 REMARK 500 ARG B 264 127.22 67.50 REMARK 500 HIS B 266 59.63 -108.37 REMARK 500 PRO B 274 54.51 -104.05 REMARK 500 TYR B 282 119.77 79.13 REMARK 500 GLU B 284 156.16 -49.70 REMARK 500 LEU B 286 151.52 88.82 REMARK 500 ALA B 299 -39.95 83.39 REMARK 500 ASP B 306 130.05 72.78 REMARK 500 TYR B 312 124.58 -34.98 REMARK 500 TYR B 357 17.41 -147.93 REMARK 500 PRO B 364 131.62 -22.35 REMARK 500 PHE B 404 48.16 -147.13 REMARK 500 ASP B 438 -127.43 40.96 REMARK 500 HIS C 37 14.01 -140.22 REMARK 500 ASP C 39 46.38 78.58 REMARK 500 LEU C 44 -60.96 -154.54 REMARK 500 ARG C 48 -50.11 70.00 REMARK 500 ASN C 59 48.20 87.69 REMARK 500 ILE C 66 153.13 -42.02 REMARK 500 ARG C 88 137.99 -28.95 REMARK 500 ASP C 90 -8.17 -56.37 REMARK 500 GLN C 96 -163.56 59.45 REMARK 500 REMARK 500 THIS ENTRY HAS 77 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 ASP B 98 ALA B 99 148.27 REMARK 500 PRO C 263 ARG C 264 149.15 REMARK 500 ALA C 273 PRO C 274 -147.29 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 ARG A3342 0.11 SIDE CHAIN REMARK 500 ARG A3362 0.09 SIDE CHAIN REMARK 500 TYR A3369 0.09 SIDE CHAIN REMARK 500 TYR A3400 0.08 SIDE CHAIN REMARK 500 ARG A3406 0.10 SIDE CHAIN REMARK 500 ARG A3411 0.09 SIDE CHAIN REMARK 500 TYR B 24 0.11 SIDE CHAIN REMARK 500 HIS B 28 0.09 SIDE CHAIN REMARK 500 ARG B 64 0.12 SIDE CHAIN REMARK 500 ARG B 79 0.15 SIDE CHAIN REMARK 500 TYR B 83 0.13 SIDE CHAIN REMARK 500 TYR B 103 0.12 SIDE CHAIN REMARK 500 ARG B 105 0.11 SIDE CHAIN REMARK 500 TYR B 161 0.09 SIDE CHAIN REMARK 500 TYR B 210 0.08 SIDE CHAIN REMARK 500 ARG B 214 0.14 SIDE CHAIN REMARK 500 ARG B 221 0.16 SIDE CHAIN REMARK 500 TYR B 224 0.09 SIDE CHAIN REMARK 500 ARG B 243 0.14 SIDE CHAIN REMARK 500 TYR B 272 0.10 SIDE CHAIN REMARK 500 ARG B 308 0.11 SIDE CHAIN REMARK 500 PHE B 343 0.07 SIDE CHAIN REMARK 500 ARG B 373 0.12 SIDE CHAIN REMARK 500 ARG B 390 0.08 SIDE CHAIN REMARK 500 TYR B 432 0.10 SIDE CHAIN REMARK 500 TYR C 36 0.08 SIDE CHAIN REMARK 500 HIS C 37 0.09 SIDE CHAIN REMARK 500 TYR C 52 0.11 SIDE CHAIN REMARK 500 TYR C 53 0.11 SIDE CHAIN REMARK 500 ARG C 79 0.10 SIDE CHAIN REMARK 500 ARG C 88 0.14 SIDE CHAIN REMARK 500 ARG C 123 0.10 SIDE CHAIN REMARK 500 ARG C 158 0.13 SIDE CHAIN REMARK 500 TYR C 161 0.10 SIDE CHAIN REMARK 500 TYR C 185 0.09 SIDE CHAIN REMARK 500 PHE C 267 0.09 SIDE CHAIN REMARK 500 TYR C 283 0.07 SIDE CHAIN REMARK 500 ARG C 369 0.14 SIDE CHAIN REMARK 500 ARG C 400 0.17 SIDE CHAIN REMARK 500 TYR C 432 0.11 SIDE CHAIN REMARK 500 TYR C 435 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3J1T RELATED DB: PDB REMARK 900 RELATED ID: EMD-5439 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHAINS B AND C ARE DERIVED FROM PDB ENTRY 1JFF. AS A RESULT, THE REMARK 999 MODELED SEQUENCES ARE FROM SUS SCROFA (UNP P02550 AND P02554, REMARK 999 RESPECTIVELY). CHAIN A IS A CHIMERA COMPRISING THE 34 N-TERMINAL REMARK 999 RESIDUES OF THERMUS THERMOPHILUS SERYL TRNA SYNTHETASE, THE REMARK 999 MICROTUBULE BINDING DOMAIN (UNP RESIDUES 3264-3427) OF MUS MUSCULUS REMARK 999 DYNEIN, THE 326 C-TERMINAL RESIDUES OF THERMUS THERMOPHILUS SERYL REMARK 999 TRNA SYNTHETASE, AND A C-TERMINAL EXPRESSION TAG REMARK 999 (GAAEQKLISEEDLNGLEHHHHHHHH). IN THIS ENTRY, ONLY THE DYNEIN REMARK 999 RESIDUES WERE MODELED. THE FULL EXPERIMENTAL SEQUENCE WAS AS REMARK 999 FOLLOWS: REMARK 999 MVDLKRLRQEPEVFHRAIREKGVALDLEALLAVDKQQEVIADKQMSVKEDLDKVEPAVIEA QNAVKS REMARK 999 IKKQHLVEVRSMANPPAAVKLALESICLLLGESTTDWKQIRSIIMRENFIPTIVN FSAEEISDAIRE REMARK 999 KMKKNYMSNPSYNYEIVNRASLACGPMVKWAIAQLNYADMLKRVEPLRN ELQKLEDDAKDNQQKLEA REMARK 999 LLLQVPLPPWPGAPVGGEEANREIKRVGGPPEFSFPPLDHVAL MEKNGWWEPRASQDSGSRSYALKG REMARK 999 DLASYEEALLRFAADFMARRGFTPADTPSRAREKAFL GTGHFPAYRDQVRAESETDTYTTGTAEVVL REMARK 999 NALHSGEILPYEALPLRYAGYAPAFRSEAGS FGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQE REMARK 999 LLENAEEILRLLELPYRLVEVATGD MGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRANLRY REMARK 999 REMARK 999 RDPEGRVRYAYTLNNTALA TPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPGAAEQKLISEED DBREF 3J1U A 3264 3427 UNP Q9JHU4 DYHC1_MOUSE 3264 3427 DBREF 3J1U B 1 451 PDB 3J1U 3J1U 1 451 DBREF 3J1U C 1 437 PDB 3J1U 3J1U 1 437 SEQRES 1 A 164 LYS GLN GLN GLU VAL ILE ALA ASP LYS GLN MET SER VAL SEQRES 2 A 164 LYS GLU ASP LEU ASP LYS VAL GLU PRO ALA VAL ILE GLU SEQRES 3 A 164 ALA GLN ASN ALA VAL LYS SER ILE LYS LYS GLN HIS LEU SEQRES 4 A 164 VAL GLU VAL ARG SER MET ALA ASN PRO PRO ALA ALA VAL SEQRES 5 A 164 LYS LEU ALA LEU GLU SER ILE CYS LEU LEU LEU GLY GLU SEQRES 6 A 164 SER THR THR ASP TRP LYS GLN ILE ARG SER ILE ILE MET SEQRES 7 A 164 ARG GLU ASN PHE ILE PRO THR ILE VAL ASN PHE SER ALA SEQRES 8 A 164 GLU GLU ILE SER ASP ALA ILE ARG GLU LYS MET LYS LYS SEQRES 9 A 164 ASN TYR MET SER ASN PRO SER TYR ASN TYR GLU ILE VAL SEQRES 10 A 164 ASN ARG ALA SER LEU ALA CYS GLY PRO MET VAL LYS TRP SEQRES 11 A 164 ALA ILE ALA GLN LEU ASN TYR ALA ASP MET LEU LYS ARG SEQRES 12 A 164 VAL GLU PRO LEU ARG ASN GLU LEU GLN LYS LEU GLU ASP SEQRES 13 A 164 ASP ALA LYS ASP ASN GLN GLN LYS SEQRES 1 B 451 MET ARG GLU CYS ILE SER ILE HIS VAL GLY GLN ALA GLY SEQRES 2 B 451 VAL GLN ILE GLY ASN ALA CYS TRP GLU LEU TYR CYS LEU SEQRES 3 B 451 GLU HIS GLY ILE GLN PRO ASP GLY GLN MET PRO SER ASP SEQRES 4 B 451 LYS THR ILE GLY GLY GLY ASP ASP SER PHE ASN THR PHE SEQRES 5 B 451 PHE SER GLU THR GLY ALA GLY LYS HIS VAL PRO ARG ALA SEQRES 6 B 451 VAL PHE VAL ASP LEU GLU PRO THR VAL ILE ASP GLU VAL SEQRES 7 B 451 ARG THR GLY THR TYR ARG GLN LEU PHE HIS PRO GLU GLN SEQRES 8 B 451 LEU ILE THR GLY LYS GLU ASP ALA ALA ASN ASN TYR ALA SEQRES 9 B 451 ARG GLY HIS TYR THR ILE GLY LYS GLU ILE ILE ASP LEU SEQRES 10 B 451 VAL LEU ASP ARG ILE ARG LYS LEU ALA ASP GLN CYS THR SEQRES 11 B 451 GLY LEU GLN GLY PHE SER VAL PHE HIS SER PHE GLY GLY SEQRES 12 B 451 GLY THR GLY SER GLY PHE THR SER LEU LEU MET GLU ARG SEQRES 13 B 451 LEU SER VAL ASP TYR GLY LYS LYS SER LYS LEU GLU PHE SEQRES 14 B 451 SER ILE TYR PRO ALA PRO GLN VAL SER THR ALA VAL VAL SEQRES 15 B 451 GLU PRO TYR ASN SER ILE LEU THR THR HIS THR THR LEU SEQRES 16 B 451 GLU HIS SER ASP CYS ALA PHE MET VAL ASP ASN GLU ALA SEQRES 17 B 451 ILE TYR ASP ILE CYS ARG ARG ASN LEU ASP ILE GLU ARG SEQRES 18 B 451 PRO THR TYR THR ASN LEU ASN ARG LEU ILE GLY GLN ILE SEQRES 19 B 451 VAL SER SER ILE THR ALA SER LEU ARG PHE ASP GLY ALA SEQRES 20 B 451 LEU ASN VAL ASP LEU THR GLU PHE GLN THR ASN LEU VAL SEQRES 21 B 451 PRO TYR PRO ARG GLY HIS PHE PRO LEU ALA THR TYR ALA SEQRES 22 B 451 PRO VAL ILE SER ALA GLU LYS ALA TYR HIS GLU GLN LEU SEQRES 23 B 451 SER VAL ALA GLU ILE THR ASN ALA CYS PHE GLU PRO ALA SEQRES 24 B 451 ASN GLN MET VAL LYS CYS ASP PRO ARG HIS GLY LYS TYR SEQRES 25 B 451 MET ALA CYS CYS LEU LEU TYR ARG GLY ASP VAL VAL PRO SEQRES 26 B 451 LYS ASP VAL ASN ALA ALA ILE ALA THR ILE LYS THR LYS SEQRES 27 B 451 ARG THR ILE GLN PHE VAL ASP TRP CYS PRO THR GLY PHE SEQRES 28 B 451 LYS VAL GLY ILE ASN TYR GLU PRO PRO THR VAL VAL PRO SEQRES 29 B 451 GLY GLY ASP LEU ALA LYS VAL GLN ARG ALA VAL CYS MET SEQRES 30 B 451 LEU SER ASN THR THR ALA ILE ALA GLU ALA TRP ALA ARG SEQRES 31 B 451 LEU ASP HIS LYS PHE ASP LEU MET TYR ALA LYS ARG ALA SEQRES 32 B 451 PHE VAL HIS TRP TYR VAL GLY GLU GLY MET GLU GLU GLY SEQRES 33 B 451 GLU PHE SER GLU ALA ARG GLU ASP MET ALA ALA LEU GLU SEQRES 34 B 451 LYS ASP TYR GLU GLU VAL GLY VAL ASP SER VAL GLU GLY SEQRES 35 B 451 GLU GLY GLU GLU GLU GLY GLU GLU TYR SEQRES 1 C 427 MET ARG GLU ILE VAL HIS ILE GLN ALA GLY GLN CYS GLY SEQRES 2 C 427 ASN GLN ILE GLY ALA LYS PHE TRP GLU VAL ILE SER ASP SEQRES 3 C 427 GLU HIS GLY ILE ASP PRO THR GLY SER TYR HIS GLY ASP SEQRES 4 C 427 SER ASP LEU GLN LEU GLU ARG ILE ASN VAL TYR TYR ASN SEQRES 5 C 427 GLU ALA ALA GLY ASN LYS TYR VAL PRO ARG ALA ILE LEU SEQRES 6 C 427 VAL ASP LEU GLU PRO GLY THR MET ASP SER VAL ARG SER SEQRES 7 C 427 GLY PRO PHE GLY GLN ILE PHE ARG PRO ASP ASN PHE VAL SEQRES 8 C 427 PHE GLY GLN SER GLY ALA GLY ASN ASN TRP ALA LYS GLY SEQRES 9 C 427 HIS TYR THR GLU GLY ALA GLU LEU VAL ASP SER VAL LEU SEQRES 10 C 427 ASP VAL VAL ARG LYS GLU SER GLU SER CYS ASP CYS LEU SEQRES 11 C 427 GLN GLY PHE GLN LEU THR HIS SER LEU GLY GLY GLY THR SEQRES 12 C 427 GLY SER GLY MET GLY THR LEU LEU ILE SER LYS ILE ARG SEQRES 13 C 427 GLU GLU TYR PRO ASP ARG ILE MET ASN THR PHE SER VAL SEQRES 14 C 427 VAL PRO SER PRO LYS VAL SER ASP THR VAL VAL GLU PRO SEQRES 15 C 427 TYR ASN ALA THR LEU SER VAL HIS GLN LEU VAL GLU ASN SEQRES 16 C 427 THR ASP GLU THR TYR CYS ILE ASP ASN GLU ALA LEU TYR SEQRES 17 C 427 ASP ILE CYS PHE ARG THR LEU LYS LEU THR THR PRO THR SEQRES 18 C 427 TYR GLY ASP LEU ASN HIS LEU VAL SER ALA THR MET SER SEQRES 19 C 427 GLY VAL THR THR CYS LEU ARG PHE PRO GLY GLN LEU ASN SEQRES 20 C 427 ALA ASP LEU ARG LYS LEU ALA VAL ASN MET VAL PRO PHE SEQRES 21 C 427 PRO ARG LEU HIS PHE PHE MET PRO GLY PHE ALA PRO LEU SEQRES 22 C 427 THR SER ARG GLY SER GLN GLN TYR ARG ALA LEU THR VAL SEQRES 23 C 427 PRO GLU LEU THR GLN GLN MET PHE ASP ALA LYS ASN MET SEQRES 24 C 427 MET ALA ALA CYS ASP PRO ARG HIS GLY ARG TYR LEU THR SEQRES 25 C 427 VAL ALA ALA VAL PHE ARG GLY ARG MET SER MET LYS GLU SEQRES 26 C 427 VAL ASP GLU GLN MET LEU ASN VAL GLN ASN LYS ASN SER SEQRES 27 C 427 SER TYR PHE VAL GLU TRP ILE PRO ASN ASN VAL LYS THR SEQRES 28 C 427 ALA VAL CYS ASP ILE PRO PRO ARG GLY LEU LYS MET SER SEQRES 29 C 427 ALA THR PHE ILE GLY ASN SER THR ALA ILE GLN GLU LEU SEQRES 30 C 427 PHE LYS ARG ILE SER GLU GLN PHE THR ALA MET PHE ARG SEQRES 31 C 427 ARG LYS ALA PHE LEU HIS TRP TYR THR GLY GLU GLY MET SEQRES 32 C 427 ASP GLU MET GLU PHE THR GLU ALA GLU SER ASN MET ASN SEQRES 33 C 427 ASP LEU VAL SER GLU TYR GLN GLN TYR GLN ASP HELIX 1 1 GLN A 3265 SER A 3296 1 32 HELIX 2 2 LYS A 3299 MET A 3308 1 10 HELIX 3 3 PRO A 3312 GLY A 3327 1 16 HELIX 4 4 ASP A 3332 ARG A 3337 1 6 HELIX 5 5 SER A 3338 ARG A 3342 5 5 HELIX 6 6 ASN A 3344 ASN A 3351 1 8 HELIX 7 7 SER A 3358 TYR A 3369 1 12 HELIX 8 8 ASN A 3372 TYR A 3375 5 4 HELIX 9 9 ASN A 3376 SER A 3384 1 9 HELIX 10 10 CYS A 3387 LYS A 3427 1 41 HELIX 11 11 GLY B 10 GLY B 29 1 20 HELIX 12 12 GLU B 71 GLY B 81 1 11 HELIX 13 13 ASN B 102 TYR B 108 1 7 HELIX 14 14 ILE B 114 GLN B 128 1 15 HELIX 15 15 GLY B 143 GLY B 162 1 20 HELIX 16 16 GLU B 183 SER B 198 1 16 HELIX 17 17 ASP B 205 ASN B 216 1 12 HELIX 18 18 THR B 223 ARG B 243 1 21 HELIX 19 19 ASP B 251 VAL B 260 1 10 HELIX 20 20 ILE B 276 ALA B 281 1 6 HELIX 21 21 SER B 287 PHE B 296 1 10 HELIX 22 22 VAL B 324 ARG B 339 1 16 HELIX 23 23 ILE B 384 ALA B 400 1 17 HELIX 24 24 VAL B 405 GLU B 411 1 7 HELIX 25 25 GLU B 414 VAL B 437 1 24 HELIX 26 26 GLY C 10 HIS C 28 1 19 HELIX 27 27 SER C 40 LEU C 44 5 5 HELIX 28 28 ARG C 48 VAL C 51 5 4 HELIX 29 29 GLU C 71 GLY C 81 1 11 HELIX 30 30 ARG C 88 ASP C 90 5 3 HELIX 31 31 ASN C 102 TYR C 108 1 7 HELIX 32 32 TYR C 108 GLU C 127 1 20 HELIX 33 33 GLY C 142 TYR C 161 1 20 HELIX 34 34 VAL C 182 ASN C 197 1 16 HELIX 35 35 ASN C 206 THR C 216 1 11 HELIX 36 36 THR C 223 LEU C 242 1 20 HELIX 37 37 ASP C 251 VAL C 260 1 10 HELIX 38 38 THR C 287 PHE C 296 1 10 HELIX 39 39 SER C 324 SER C 340 1 17 HELIX 40 40 ILE C 384 LYS C 402 1 19 HELIX 41 41 LEU C 405 GLY C 410 1 6 HELIX 42 42 ASP C 414 ASP C 437 1 24 SHEET 1 A 6 LEU B 92 THR B 94 0 SHEET 2 A 6 ALA B 65 ASP B 69 1 N PHE B 67 O ILE B 93 SHEET 3 A 6 SER B 6 HIS B 8 1 N SER B 6 O VAL B 66 SHEET 4 A 6 GLY B 134 PHE B 138 1 O PHE B 138 N ILE B 7 SHEET 5 A 6 SER B 165 ILE B 171 1 O LEU B 167 N VAL B 137 SHEET 6 A 6 CYS B 200 VAL B 204 1 O VAL B 204 N SER B 170 SHEET 1 B 4 LEU B 269 TYR B 272 0 SHEET 2 B 4 CYS B 376 THR B 381 -1 O MET B 377 N THR B 271 SHEET 3 B 4 TYR B 312 TYR B 319 -1 N LEU B 318 O CYS B 376 SHEET 4 B 4 VAL B 353 ILE B 355 1 O GLY B 354 N LEU B 317 SHEET 1 C 4 VAL C 5 ALA C 9 0 SHEET 2 C 4 PHE C 135 SER C 140 1 O THR C 138 N ALA C 9 SHEET 3 C 4 MET C 166 VAL C 172 1 O VAL C 171 N HIS C 139 SHEET 4 C 4 THR C 201 ASP C 205 1 O TYR C 202 N THR C 168 SHEET 1 D 2 TYR C 53 ALA C 56 0 SHEET 2 D 2 LYS C 60 PRO C 63 -1 O LYS C 60 N ALA C 56 SHEET 1 E 2 LEU C 67 VAL C 68 0 SHEET 2 E 2 PHE C 92 VAL C 93 1 O VAL C 93 N LEU C 67 SHEET 1 F 4 PHE C 268 PHE C 272 0 SHEET 2 F 4 SER C 374 ASN C 380 -1 O GLY C 379 N MET C 269 SHEET 3 F 4 VAL C 315 ARG C 320 -1 N ALA C 316 O ILE C 378 SHEET 4 F 4 VAL C 351 CYS C 356 1 O ALA C 354 N PHE C 319 CISPEP 1 MET B 1 ARG B 2 0 -9.78 CISPEP 2 GLY B 34 GLN B 35 0 7.56 CISPEP 3 ASP B 39 LYS B 40 0 -3.47 CISPEP 4 GLY B 44 GLY B 45 0 6.07 CISPEP 5 PHE B 49 ASN B 50 0 -15.08 CISPEP 6 THR B 51 PHE B 52 0 10.18 CISPEP 7 HIS B 139 SER B 140 0 -15.93 CISPEP 8 GLY C 81 PRO C 82 0 27.92 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