PDB Short entry for 2N13 HEADER MOTOR PROTEIN/PROTEIN BINDING 20-MAR-15 2N13 TITLE COMPLEX STRUCTURE OF MYUB (1080-1122) OF HUMAN MYOSIN VI WITH K63-DIUB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCONVENTIONAL MYOSIN-VI; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: K63R, G76C; COMPND 5 SYNONYM: UNCONVENTIONAL MYOSIN-6; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: UBIQUITIN; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: UBIQUITIN; COMPND 14 CHAIN: C; 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: KIAA0389, MYO6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX6P; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: UBB; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET3A; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 GENE: UBB; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 24 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS MOTOR PROTEIN-PROTEIN BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.HE,K.WALTERS REVDAT 4 14-JUN-23 2N13 1 REMARK SEQADV LINK REVDAT 3 06-APR-16 2N13 1 JRNL REVDAT 2 30-MAR-16 2N13 1 JRNL REVDAT 1 09-MAR-16 2N13 0 JRNL AUTH F.HE,H.P.WOLLSCHEID,U.NOWICKA,M.BIANCOSPINO,E.VALENTINI, JRNL AUTH 2 A.EHLINGER,F.ACCONCIA,E.MAGISTRATI,S.POLO,K.J.WALTERS JRNL TITL MYOSIN VI CONTAINS A COMPACT STRUCTURAL MOTIF THAT BINDS TO JRNL TITL 2 UBIQUITIN CHAINS. JRNL REF CELL REP V. 14 2683 2016 JRNL REFN ESSN 2211-1247 JRNL PMID 26971995 JRNL DOI 10.1016/J.CELREP.2016.01.079 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000104288. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] PROTEIN, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HALF-FILTER NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : KUJIRA, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 HH TYR A 20 H GLY B 176 1.34 REMARK 500 O LEU D 335 H CYS D 339 1.56 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 1 THR A 10 132.00 -171.96 REMARK 500 1 LYS A 11 120.06 59.37 REMARK 500 1 LYS A 12 -156.79 -74.83 REMARK 500 1 LEU A 15 37.76 -91.20 REMARK 500 1 THR A 29 -2.58 -145.49 REMARK 500 1 ILE A 33 -38.57 -39.56 REMARK 500 1 TYR A 50 99.22 -162.73 REMARK 500 1 GLU B 134 -108.11 -86.11 REMARK 500 1 ARG B 142 105.96 -170.42 REMARK 500 1 ALA B 146 27.14 40.78 REMARK 500 1 ASP B 158 10.68 -69.41 REMARK 500 1 TYR B 159 13.05 -140.72 REMARK 500 1 GLN B 162 -156.94 -80.02 REMARK 500 1 ARG B 172 103.03 -57.73 REMARK 500 1 GLU C 234 -107.00 -85.38 REMARK 500 1 PHE C 245 77.41 -105.71 REMARK 500 1 ALA C 246 89.14 62.21 REMARK 500 1 LEU C 256 -3.63 -57.87 REMARK 500 1 ILE C 261 94.21 -61.74 REMARK 500 1 GLN C 262 -156.37 -76.95 REMARK 500 1 LYS D 311 94.22 40.35 REMARK 500 1 LEU D 315 33.65 -95.09 REMARK 500 1 LYS D 317 26.52 -144.37 REMARK 500 1 ASP D 332 93.85 -66.35 REMARK 500 1 LYS D 348 -72.15 -63.83 REMARK 500 1 TYR D 350 25.86 -156.15 REMARK 500 2 THR A 10 -155.20 -87.92 REMARK 500 2 LEU A 15 43.70 -91.31 REMARK 500 2 THR A 29 -40.74 -135.45 REMARK 500 2 ASP A 32 99.70 -162.42 REMARK 500 2 ILE A 33 -36.69 -39.87 REMARK 500 2 VAL B 117 -162.37 -119.54 REMARK 500 2 GLU B 134 -117.06 -79.93 REMARK 500 2 ARG B 142 132.16 -170.32 REMARK 500 2 ILE B 161 92.24 -68.40 REMARK 500 2 GLN B 162 -157.38 -78.63 REMARK 500 2 THR C 207 -150.45 -101.81 REMARK 500 2 THR C 209 23.76 -74.39 REMARK 500 2 LYS C 211 159.36 -46.14 REMARK 500 2 GLU C 234 -104.64 -85.07 REMARK 500 2 GLN C 262 -156.05 -80.79 REMARK 500 2 ARG C 272 90.64 -45.64 REMARK 500 2 ARG C 274 -155.45 -172.46 REMARK 500 2 THR D 310 79.38 -67.30 REMARK 500 2 LYS D 312 -172.52 44.57 REMARK 500 2 LEU D 315 36.62 -96.39 REMARK 500 2 LYS D 317 40.90 -146.65 REMARK 500 2 ASP D 332 91.61 -66.13 REMARK 500 2 TYR D 350 70.42 -68.45 REMARK 500 3 THR A 10 94.15 -46.82 REMARK 500 REMARK 500 THIS ENTRY HAS 464 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 1 ARG B 142 0.30 SIDE CHAIN REMARK 500 1 ARG B 154 0.31 SIDE CHAIN REMARK 500 1 ARG B 163 0.18 SIDE CHAIN REMARK 500 1 ARG B 172 0.24 SIDE CHAIN REMARK 500 1 ARG B 174 0.16 SIDE CHAIN REMARK 500 1 ARG C 272 0.30 SIDE CHAIN REMARK 500 1 ARG C 274 0.30 SIDE CHAIN REMARK 500 2 ARG B 142 0.23 SIDE CHAIN REMARK 500 2 ARG B 154 0.12 SIDE CHAIN REMARK 500 2 ARG B 163 0.28 SIDE CHAIN REMARK 500 2 ARG B 172 0.31 SIDE CHAIN REMARK 500 2 ARG B 174 0.28 SIDE CHAIN REMARK 500 2 ARG C 242 0.25 SIDE CHAIN REMARK 500 2 ARG C 254 0.10 SIDE CHAIN REMARK 500 2 ARG C 274 0.30 SIDE CHAIN REMARK 500 3 ARG B 142 0.29 SIDE CHAIN REMARK 500 3 ARG B 154 0.30 SIDE CHAIN REMARK 500 3 ARG B 163 0.16 SIDE CHAIN REMARK 500 3 ARG B 172 0.18 SIDE CHAIN REMARK 500 3 ARG B 174 0.31 SIDE CHAIN REMARK 500 3 ARG C 254 0.29 SIDE CHAIN REMARK 500 3 ARG C 272 0.10 SIDE CHAIN REMARK 500 3 ARG C 274 0.22 SIDE CHAIN REMARK 500 4 ARG B 154 0.23 SIDE CHAIN REMARK 500 4 ARG B 172 0.14 SIDE CHAIN REMARK 500 4 ARG B 174 0.28 SIDE CHAIN REMARK 500 4 ARG C 242 0.30 SIDE CHAIN REMARK 500 4 ARG C 254 0.21 SIDE CHAIN REMARK 500 4 ARG C 272 0.20 SIDE CHAIN REMARK 500 4 ARG C 274 0.16 SIDE CHAIN REMARK 500 5 ARG B 142 0.30 SIDE CHAIN REMARK 500 5 ARG B 154 0.28 SIDE CHAIN REMARK 500 5 ARG B 163 0.30 SIDE CHAIN REMARK 500 5 ARG B 172 0.28 SIDE CHAIN REMARK 500 5 ARG B 174 0.10 SIDE CHAIN REMARK 500 5 ARG C 242 0.09 SIDE CHAIN REMARK 500 5 ARG C 254 0.28 SIDE CHAIN REMARK 500 5 ARG C 272 0.16 SIDE CHAIN REMARK 500 5 ARG C 274 0.26 SIDE CHAIN REMARK 500 6 ARG B 142 0.31 SIDE CHAIN REMARK 500 6 ARG B 163 0.29 SIDE CHAIN REMARK 500 6 ARG B 172 0.28 SIDE CHAIN REMARK 500 6 ARG B 174 0.24 SIDE CHAIN REMARK 500 6 ARG C 242 0.23 SIDE CHAIN REMARK 500 6 ARG C 272 0.30 SIDE CHAIN REMARK 500 6 ARG C 274 0.29 SIDE CHAIN REMARK 500 7 ARG B 142 0.31 SIDE CHAIN REMARK 500 7 ARG B 154 0.30 SIDE CHAIN REMARK 500 7 ARG B 163 0.31 SIDE CHAIN REMARK 500 7 ARG B 172 0.12 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 159 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25545 RELATED DB: BMRB REMARK 900 RELATED ID: 2N0Z RELATED DB: PDB REMARK 900 RELATED ID: 2N10 RELATED DB: PDB REMARK 900 RELATED ID: 2N11 RELATED DB: PDB REMARK 900 RELATED ID: 2N12 RELATED DB: PDB DBREF 2N13 A 9 51 UNP Q9UM54 MYO6_HUMAN 1080 1122 DBREF 2N13 B 101 176 UNP P0CG47 UBB_HUMAN 1 76 DBREF 2N13 C 201 276 UNP P0CG47 UBB_HUMAN 1 76 DBREF 2N13 D 309 351 UNP Q9UM54 MYO6_HUMAN 1080 1122 SEQADV 2N13 ARG B 163 UNP P0CG47 LYS 63 ENGINEERED MUTATION SEQADV 2N13 CYS C 276 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQRES 1 A 43 GLY THR LYS LYS TYR ASP LEU SER LYS TRP LYS TYR ALA SEQRES 2 A 43 GLU LEU ARG ASP THR ILE ASN THR SER CYS ASP ILE GLU SEQRES 3 A 43 LEU LEU ALA ALA CYS ARG GLU GLU PHE HIS ARG ARG LEU SEQRES 4 A 43 LYS VAL TYR HIS SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY CYS SEQRES 1 D 43 GLY THR LYS LYS TYR ASP LEU SER LYS TRP LYS TYR ALA SEQRES 2 D 43 GLU LEU ARG ASP THR ILE ASN THR SER CYS ASP ILE GLU SEQRES 3 D 43 LEU LEU ALA ALA CYS ARG GLU GLU PHE HIS ARG ARG LEU SEQRES 4 D 43 LYS VAL TYR HIS HELIX 1 1 LYS A 19 SER A 30 1 12 HELIX 2 2 ASP A 32 VAL A 49 1 18 HELIX 3 3 THR B 122 GLU B 134 1 13 HELIX 4 4 PRO B 137 GLN B 141 5 5 HELIX 5 5 LEU B 156 ASN B 160 5 5 HELIX 6 6 THR C 222 GLU C 234 1 13 HELIX 7 7 PRO C 237 GLN C 241 5 5 HELIX 8 8 LYS D 319 SER D 330 1 12 HELIX 9 9 ASP D 332 VAL D 349 1 18 SHEET 1 A 5 THR B 112 GLU B 116 0 SHEET 2 A 5 GLN B 102 LYS B 106 -1 N ILE B 103 O LEU B 115 SHEET 3 A 5 THR B 166 LEU B 169 1 O LEU B 167 N PHE B 104 SHEET 4 A 5 LEU B 143 PHE B 145 -1 N ILE B 144 O HIS B 168 SHEET 5 A 5 LYS B 148 GLN B 149 -1 O LYS B 148 N PHE B 145 SHEET 1 B 4 THR C 212 GLU C 216 0 SHEET 2 B 4 GLN C 202 LYS C 206 -1 N ILE C 203 O LEU C 215 SHEET 3 B 4 THR C 266 VAL C 270 1 O LEU C 269 N LYS C 206 SHEET 4 B 4 ARG C 242 ILE C 244 -1 N ARG C 242 O VAL C 270 LINK C GLY B 176 NZ LYS C 263 1555 1555 1.33 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