PDB Short entry for 5JPW HEADER MOTOR PROTEIN 04-MAY-16 5JPW TITLE MOLECULAR BASIS FOR PROTEIN RECOGNITION SPECIFICITY OF THE TITLE 2 DYNLT1/TCTEX1 CANONICAL BINDING GROOVE. CHARACTERIZATION OF THE TITLE 3 INTERACTION WITH ACTIVIN RECEPTOR IIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYNEIN LIGHT CHAIN TCTEX-TYPE 1,CYTOPLASMIC DYNEIN 1 COMPND 3 INTERMEDIATE CHAIN 2; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUES 1-113,UNP RESIDUES 134-154; COMPND 6 SYNONYM: PROTEIN CW-1,T-COMPLEX TESTIS-SPECIFIC PROTEIN 1 HOMOLOG, COMPND 7 CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN 2,DYNEIN INTERMEDIATE CHAIN 2, COMPND 8 CYTOSOLIC,DH IC-2; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: RESIDUES G1 TO S2 CORRESPOND TO THE EXPRESSION TAG. COMPND 11 RESIDUES M3 TO I115 CORRESPOND TO THE WHOLE SEQUENCE OF DYNEIN LIGHT COMPND 12 CHAIN TCTEX-TYPE 1 (H. SAPIENS, UNIPROT ENTRY P63172). RESIDUES G116 COMPND 13 TO S122 CORRESPOND TO A DESIGNED LINKER SEQUENCE. RESIDUES G123 TO COMPND 14 V143 CORRESPOND TO RESIDUES G134 TO V154 OF CYTOPLASMIC DYNEIN 1 COMPND 15 INTERMEDIATE CHAIN 2 (H. SAPIENS, UNIPROT ENTRY Q13409) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DYNLT1, TCTEL1, TCTEX-1, TCTEX1, DYNC1I2, DNCI2, DNCIC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNYLT1/TCTEX-1; DYNEIN INTERMEDIATE CHAIN; DYNEIN MOTOR; DYNEIN- KEYWDS 2 MEDIATED TRANSPORT, MOTOR PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.RODRIGUEZ-CRESPO,J.MERINO-GRACIA,M.BRUIX,H.ZAMORA-CARRERAS REVDAT 6 14-JUN-23 5JPW 1 REMARK REVDAT 5 08-MAY-19 5JPW 1 REMARK REVDAT 4 06-SEP-17 5JPW 1 REMARK REVDAT 3 19-OCT-16 5JPW 1 JRNL REVDAT 2 28-SEP-16 5JPW 1 REVDAT 1 17-AUG-16 5JPW 0 JRNL AUTH J.MERINO-GRACIA,H.ZAMORA-CARRERAS,M.BRUIX,I.RODRIGUEZ-CRESPO JRNL TITL MOLECULAR BASIS FOR THE PROTEIN RECOGNITION SPECIFICITY OF JRNL TITL 2 THE DYNEIN LIGHT CHAIN DYNLT1/TCTEX1: CHARACTERIZATION OF JRNL TITL 3 THE INTERACTION WITH ACTIVIN RECEPTOR IIB. JRNL REF J.BIOL.CHEM. V. 291 20962 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27502274 JRNL DOI 10.1074/JBC.M116.736884 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000220837. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 100 UM DYNLT1/TCTEX1-DIC REMARK 210 CHIMERA, 100 MM POTASSIUM REMARK 210 PHOSPHATE, 1 MM DTT, 50 UM DSS, REMARK 210 90% H2O/10% D2O; 100 UM [U-99% REMARK 210 15N] DYNLT1/TCTEX1-DIC CHIMERA, REMARK 210 100 MM POTASSIUM PHOSPHATE, 1 MM REMARK 210 DTT, 50 UM DSS, 90% H2O/10% D2O; REMARK 210 100 UM [U-99% 13C; U-99% 15N] REMARK 210 DYNLT1/TCTEX1-DIC CHIMERA, 100 REMARK 210 MM POTASSIUM PHOSPHATE, 1 MM DTT, REMARK 210 50 UM DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 1 SER A 2 46.37 -97.23 REMARK 500 1 HIS A 38 -66.01 -106.44 REMARK 500 1 SER A 84 35.32 -76.95 REMARK 500 1 SER A 89 -60.47 -123.51 REMARK 500 1 SER B 145 49.79 -84.29 REMARK 500 1 HIS B 181 -65.96 -106.32 REMARK 500 1 SER B 227 35.52 -76.96 REMARK 500 1 SER B 232 -61.74 -120.50 REMARK 500 2 ASN A 34 -175.79 -68.61 REMARK 500 2 ALA A 35 107.83 -52.16 REMARK 500 2 LYS A 64 92.60 -69.17 REMARK 500 2 SER A 84 22.14 -73.91 REMARK 500 2 SER A 89 -56.57 -135.05 REMARK 500 2 ASP A 92 -164.54 -161.42 REMARK 500 2 SER A 119 -163.91 -124.67 REMARK 500 2 ARG A 140 -57.05 -160.98 REMARK 500 2 ASN B 177 -175.70 -68.72 REMARK 500 2 ALA B 178 107.83 -52.21 REMARK 500 2 SER B 227 23.22 -74.11 REMARK 500 2 SER B 232 -61.09 -127.14 REMARK 500 2 ASP B 235 -163.79 -162.04 REMARK 500 2 SER B 262 -164.35 -125.62 REMARK 500 2 ARG B 283 -57.45 -160.49 REMARK 500 3 ALA A 9 19.33 -66.71 REMARK 500 3 HIS A 38 -88.30 -84.09 REMARK 500 3 ALA A 77 -169.94 -73.06 REMARK 500 3 SER A 89 -66.31 -109.24 REMARK 500 3 GLN A 121 177.64 -58.13 REMARK 500 3 ARG A 140 -53.99 -159.10 REMARK 500 3 ALA B 152 19.17 -66.50 REMARK 500 3 HIS B 181 -99.15 -96.47 REMARK 500 3 SER B 232 -66.42 -108.59 REMARK 500 3 GLN B 264 177.74 -58.56 REMARK 500 3 ARG B 283 -53.97 -159.40 REMARK 500 4 ALA A 8 51.07 -97.81 REMARK 500 4 ALA A 9 0.37 -69.14 REMARK 500 4 HIS A 38 -118.12 -95.37 REMARK 500 4 SER A 39 0.47 -66.75 REMARK 500 4 LYS A 64 75.91 -100.19 REMARK 500 4 LYS A 74 -58.57 -146.72 REMARK 500 4 SER A 89 -57.29 -134.47 REMARK 500 4 MET A 129 93.13 -63.82 REMARK 500 4 ARG A 140 -61.04 -160.19 REMARK 500 4 ALA B 151 51.14 -97.60 REMARK 500 4 ALA B 152 0.33 -69.21 REMARK 500 4 HIS B 181 -117.66 -95.46 REMARK 500 4 SER B 182 0.39 -66.76 REMARK 500 4 LYS B 217 -63.92 -143.03 REMARK 500 4 SER B 232 -59.75 -128.74 REMARK 500 4 MET B 272 97.91 -62.79 REMARK 500 REMARK 500 THIS ENTRY HAS 258 RAMACHANDRAN OUTLIERS. 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 5 TYR B 208 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30074 RELATED DB: BMRB DBREF 5JPW A 3 115 UNP P63172 DYLT1_HUMAN 1 113 DBREF 5JPW A 123 143 UNP Q13409 DC1I2_HUMAN 134 154 DBREF 5JPW B 146 258 UNP P63172 DYLT1_HUMAN 1 113 DBREF 5JPW B 266 286 UNP Q13409 DC1I2_HUMAN 134 154 SEQADV 5JPW GLY A 1 UNP P63172 EXPRESSION TAG SEQADV 5JPW SER A 2 UNP P63172 EXPRESSION TAG SEQADV 5JPW GLY A 116 UNP P63172 LINKER SEQADV 5JPW GLY A 117 UNP P63172 LINKER SEQADV 5JPW GLY A 118 UNP P63172 LINKER SEQADV 5JPW SER A 119 UNP P63172 LINKER SEQADV 5JPW GLY A 120 UNP P63172 LINKER SEQADV 5JPW GLN A 121 UNP P63172 LINKER SEQADV 5JPW SER A 122 UNP P63172 LINKER SEQADV 5JPW GLY B 144 UNP P63172 EXPRESSION TAG SEQADV 5JPW SER B 145 UNP P63172 EXPRESSION TAG SEQADV 5JPW GLY B 259 UNP P63172 LINKER SEQADV 5JPW GLY B 260 UNP P63172 LINKER SEQADV 5JPW GLY B 261 UNP P63172 LINKER SEQADV 5JPW SER B 262 UNP P63172 LINKER SEQADV 5JPW GLY B 263 UNP P63172 LINKER SEQADV 5JPW GLN B 264 UNP P63172 LINKER SEQADV 5JPW SER B 265 UNP P63172 LINKER SEQRES 1 A 143 GLY SER MET GLU ASP TYR GLN ALA ALA GLU GLU THR ALA SEQRES 2 A 143 PHE VAL VAL ASP GLU VAL SER ASN ILE VAL LYS GLU ALA SEQRES 3 A 143 ILE GLU SER ALA ILE GLY GLY ASN ALA TYR GLN HIS SER SEQRES 4 A 143 LYS VAL ASN GLN TRP THR THR ASN VAL VAL GLU GLN THR SEQRES 5 A 143 LEU SER GLN LEU THR LYS LEU GLY LYS PRO PHE LYS TYR SEQRES 6 A 143 ILE VAL THR CYS VAL ILE MET GLN LYS ASN GLY ALA GLY SEQRES 7 A 143 LEU HIS THR ALA SER SER CYS PHE TRP ASP SER SER THR SEQRES 8 A 143 ASP GLY SER CYS THR VAL ARG TRP GLU ASN LYS THR MET SEQRES 9 A 143 TYR CYS ILE VAL SER ALA PHE GLY LEU SER ILE GLY GLY SEQRES 10 A 143 GLY SER GLY GLN SER GLY PRO ILE LYS LEU GLY MET ALA SEQRES 11 A 143 LYS ILE THR GLN VAL ASP PHE PRO PRO ARG GLU ILE VAL SEQRES 1 B 143 GLY SER MET GLU ASP TYR GLN ALA ALA GLU GLU THR ALA SEQRES 2 B 143 PHE VAL VAL ASP GLU VAL SER ASN ILE VAL LYS GLU ALA SEQRES 3 B 143 ILE GLU SER ALA ILE GLY GLY ASN ALA TYR GLN HIS SER SEQRES 4 B 143 LYS VAL ASN GLN TRP THR THR ASN VAL VAL GLU GLN THR SEQRES 5 B 143 LEU SER GLN LEU THR LYS LEU GLY LYS PRO PHE LYS TYR SEQRES 6 B 143 ILE VAL THR CYS VAL ILE MET GLN LYS ASN GLY ALA GLY SEQRES 7 B 143 LEU HIS THR ALA SER SER CYS PHE TRP ASP SER SER THR SEQRES 8 B 143 ASP GLY SER CYS THR VAL ARG TRP GLU ASN LYS THR MET SEQRES 9 B 143 TYR CYS ILE VAL SER ALA PHE GLY LEU SER ILE GLY GLY SEQRES 10 B 143 GLY SER GLY GLN SER GLY PRO ILE LYS LEU GLY MET ALA SEQRES 11 B 143 LYS ILE THR GLN VAL ASP PHE PRO PRO ARG GLU ILE VAL HELIX 1 AA1 SER A 2 TYR A 6 5 5 HELIX 2 AA2 VAL A 15 GLY A 32 1 18 HELIX 3 AA3 SER A 39 GLY A 60 1 22 HELIX 4 AA4 SER B 145 TYR B 149 5 5 HELIX 5 AA5 VAL B 158 GLY B 175 1 18 HELIX 6 AA6 SER B 182 GLY B 203 1 22 SHEET 1 AA1 5 GLY A 93 GLU A 100 0 SHEET 2 AA1 5 MET A 104 LEU A 113 -1 O VAL A 108 N VAL A 97 SHEET 3 AA1 5 LYS A 64 GLN A 73 -1 N THR A 68 O SER A 109 SHEET 4 AA1 5 HIS B 223 SER B 226 -1 O ALA B 225 N CYS A 69 SHEET 5 AA1 5 THR B 276 ASP B 279 -1 O VAL B 278 N THR B 224 SHEET 1 AA2 5 THR A 133 ASP A 136 0 SHEET 2 AA2 5 HIS A 80 SER A 83 -1 N THR A 81 O VAL A 135 SHEET 3 AA2 5 LYS B 207 GLN B 216 -1 O CYS B 212 N ALA A 82 SHEET 4 AA2 5 MET B 247 LEU B 256 -1 O SER B 252 N THR B 211 SHEET 5 AA2 5 GLY B 236 GLU B 243 -1 N VAL B 240 O VAL B 251 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