1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Swanson, K.A. Kang, R.S. Stamenova, S.D. Hicke, L. Radhakrishnan, I. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Embo J. EMJODG 0897 0261-4189 22 4597 4606 10.1093/emboj/cdg471 12970172 Solution Structure of Vps27 UIM-Ubiquitin Complex Important for Endosomal Sorting and Receptor Downregulation 2003 10.2210/pdb1q0w/pdb pdb_00001q0w 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 2824.103 Vacuolar protein sorting-associated protein VPS27 Amino-terminal UIM, residues 256 to 278 1 syn polymer 8568.769 Ubiquitin 1 man polymer no no YPEDEEELIRKAIELSLKESRNSA YPEDEEELIRKAIELSLKESRNSA A polypeptide(L) no no MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n baker's yeast Saccharomyces Escherichia Escherichia coli sample (UBI1 OR RPL40A OR YIL148W) AND (UBI2 OR RPL40B OR YKR094C) AND (UBI3 OR RPS31 OR YLR167W OR L9470.14) AND (UBI4 OR SCD2 OR YLL039C) 4932 Saccharomyces cerevisiae 469008 Escherichia coli BL21(DE3) BL21(DE3) PLASMID pET3-a database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-10-07 1 1 2008-04-29 1 2 2011-07-13 1 3 2021-10-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_ref_seq_dif.details Solution structure of tandem UIMs of Vps27 Crystal structure of the Vps27 carboxy-terminal UIM HELIX Author determined secondary structure SHEET Author determined secondary structure RCSB Y RCSB 2003-07-17 REL REL The sequence was synthesized using a peptide synthesizer. The sequence contains a non-native tyrosine residue at the amino-terminus (residue number 255). The sequence occurs naturally in S. Cerevisiae. sample The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry 80 20 3D_15N-separated_NOESY 2D double half-filtered NOESY 3D_13C-separated_NOESY 2D double half-filtered NOESY 3D 13C-filtered,13C-edited NOESY 20 mM sodium phosphate, pH 6.0, 0.2% NaN3 6.0 1 atm 298 K THE STRUCTURES ARE BASED ON A TOTAL OF 2138 DISTANCE RESTRAINTS, INCLUDING 2062 NOE-DERIVED DISTANCE RESTRAINTS [1625 UNAMBIGUOUS AND 437 AMBIGUOUS RESTRAINTS], 76 HYDROGEN BONDING DISTANCE RESTRAINTS, AND 112 TORSION ANGLE RESTRAINTS. TORSION ANGLE DYNAMICS AND SIMULATED ANNEALING 1 closest to the average 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM 90% H2O/10% D2O 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM 100% D2O Varian Instruments collection VNMR 6.1B Accelrys data analysis Felix 98.0 Brunger et al. refinement CNS 1.1 Linge and Nilges refinement ARIA 1.2 600 Varian INOVA TYR 255 n 1 TYR 255 A PRO 256 n 2 PRO 256 A GLU 257 n 3 GLU 257 A ASP 258 n 4 ASP 258 A GLU 259 n 5 GLU 259 A GLU 260 n 6 GLU 260 A GLU 261 n 7 GLU 261 A LEU 262 n 8 LEU 262 A ILE 263 n 9 ILE 263 A ARG 264 n 10 ARG 264 A LYS 265 n 11 LYS 265 A ALA 266 n 12 ALA 266 A ILE 267 n 13 ILE 267 A GLU 268 n 14 GLU 268 A LEU 269 n 15 LEU 269 A SER 270 n 16 SER 270 A LEU 271 n 17 LEU 271 A LYS 272 n 18 LYS 272 A GLU 273 n 19 GLU 273 A SER 274 n 20 SER 274 A ARG 275 n 21 ARG 275 A ASN 276 n 22 ASN 276 A SER 277 n 23 SER 277 A ALA 278 n 24 ALA 278 A MET 1 n 1 MET 1 B GLN 2 n 2 GLN 2 B ILE 3 n 3 ILE 3 B PHE 4 n 4 PHE 4 B VAL 5 n 5 VAL 5 B LYS 6 n 6 LYS 6 B THR 7 n 7 THR 7 B LEU 8 n 8 LEU 8 B THR 9 n 9 THR 9 B GLY 10 n 10 GLY 10 B LYS 11 n 11 LYS 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B THR 14 n 14 THR 14 B LEU 15 n 15 LEU 15 B GLU 16 n 16 GLU 16 B VAL 17 n 17 VAL 17 B GLU 18 n 18 GLU 18 B SER 19 n 19 SER 19 B SER 20 n 20 SER 20 B ASP 21 n 21 ASP 21 B THR 22 n 22 THR 22 B ILE 23 n 23 ILE 23 B ASP 24 n 24 ASP 24 B ASN 25 n 25 ASN 25 B VAL 26 n 26 VAL 26 B LYS 27 n 27 LYS 27 B SER 28 n 28 SER 28 B LYS 29 n 29 LYS 29 B ILE 30 n 30 ILE 30 B GLN 31 n 31 GLN 31 B ASP 32 n 32 ASP 32 B LYS 33 n 33 LYS 33 B GLU 34 n 34 GLU 34 B GLY 35 n 35 GLY 35 B ILE 36 n 36 ILE 36 B PRO 37 n 37 PRO 37 B PRO 38 n 38 PRO 38 B ASP 39 n 39 ASP 39 B GLN 40 n 40 GLN 40 B GLN 41 n 41 GLN 41 B ARG 42 n 42 ARG 42 B LEU 43 n 43 LEU 43 B ILE 44 n 44 ILE 44 B PHE 45 n 45 PHE 45 B ALA 46 n 46 ALA 46 B GLY 47 n 47 GLY 47 B LYS 48 n 48 LYS 48 B GLN 49 n 49 GLN 49 B LEU 50 n 50 LEU 50 B GLU 51 n 51 GLU 51 B ASP 52 n 52 ASP 52 B GLY 53 n 53 GLY 53 B ARG 54 n 54 ARG 54 B THR 55 n 55 THR 55 B LEU 56 n 56 LEU 56 B SER 57 n 57 SER 57 B ASP 58 n 58 ASP 58 B TYR 59 n 59 TYR 59 B ASN 60 n 60 ASN 60 B ILE 61 n 61 ILE 61 B GLN 62 n 62 GLN 62 B LYS 63 n 63 LYS 63 B GLU 64 n 64 GLU 64 B SER 65 n 65 SER 65 B THR 66 n 66 THR 66 B LEU 67 n 67 LEU 67 B HIS 68 n 68 HIS 68 B LEU 69 n 69 LEU 69 B VAL 70 n 70 VAL 70 B LEU 71 n 71 LEU 71 B ARG 72 n 72 ARG 72 B LEU 73 n 73 LEU 73 B ARG 74 n 74 ARG 74 B GLY 75 n 75 GLY 75 B GLY 76 n 76 GLY 76 B author_defined_assembly 2 dimeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 B O ILE 13 B O ILE 13 B N VAL 5 B N VAL 5 B N LYS 6 B N LYS 6 B O LEU 67 B O LEU 67 B O HIS 68 B O HIS 68 B N ILE 44 B N ILE 44 B N PHE 45 B N PHE 45 B O LYS 48 B O LYS 48 2 B B H HD21 THR ASN 22 25 1.32 14 A B HA HG22 ILE VAL 263 70 1.34 16 A B HA HG22 ILE VAL 263 70 1.33 1 A PRO 256 -78.17 47.98 1 A GLU 257 -145.11 52.12 1 A SER 274 -80.25 41.96 1 A ASN 276 -79.97 42.22 1 B ASP 52 -76.76 49.44 2 A PRO 256 -76.94 38.96 2 A GLU 257 63.61 135.14 2 A SER 274 -81.92 47.48 2 A ASN 276 56.90 -127.05 2 A SER 277 -69.76 -140.52 2 B THR 7 -74.05 -151.50 2 B THR 9 -153.42 54.85 2 B ARG 74 -173.28 130.83 3 A ARG 275 -75.06 34.04 3 A ASN 276 -82.55 45.55 3 B LEU 8 -75.04 43.62 3 B THR 9 -149.57 33.02 3 B VAL 17 -148.80 -156.74 3 B ARG 72 -76.78 47.34 3 B LEU 73 64.40 131.91 4 B THR 22 -71.67 -152.98 4 B GLU 51 -67.35 -156.19 4 B ASP 52 -142.28 43.25 4 B LEU 73 49.52 -135.37 5 A PRO 256 -66.27 -134.70 5 A SER 274 -86.55 39.34 5 A SER 277 -80.58 41.99 5 B SER 20 -86.04 39.31 5 B ARG 74 -176.72 -44.93 6 A GLU 257 66.47 135.15 6 A SER 277 57.67 -143.98 6 B LEU 8 51.87 -103.76 6 B THR 9 -153.46 58.46 6 B LYS 33 -67.12 -70.53 6 B LEU 73 61.28 133.14 7 A SER 277 74.00 -43.43 7 B THR 9 -152.30 -46.05 7 B THR 22 -69.11 -173.47 7 B ASP 52 -76.45 49.31 8 A ARG 275 58.12 -133.15 8 A SER 277 -179.30 44.57 8 B THR 22 -78.70 -158.16 8 B GLU 51 -68.71 -148.47 8 B ASP 52 -151.30 45.34 8 B ARG 74 66.06 135.57 9 A GLU 257 -144.61 -64.78 9 A SER 274 -84.12 48.03 9 A ASN 276 -175.63 53.87 9 A SER 277 -172.61 -49.58 9 B SER 20 -92.31 39.06 9 B ASP 21 -78.27 -148.81 9 B GLU 51 -68.35 -145.82 9 B ASP 52 -163.36 49.94 9 B ARG 74 61.18 -127.39 10 A GLU 257 -146.40 45.52 10 A ARG 275 65.74 -78.85 11 A SER 274 -85.99 39.09 11 B THR 22 -71.75 -152.01 11 B GLU 51 -65.97 -146.64 11 B ASP 52 -156.49 45.03 12 A ARG 275 74.50 -41.90 12 A ASN 276 -70.06 -137.72 12 A SER 277 -171.03 48.92 12 B SER 20 -82.39 41.44 12 B LEU 73 60.39 128.61 12 B ARG 74 -173.76 131.17 13 A ASN 276 -156.56 39.30 13 B SER 20 -99.57 34.41 13 B LYS 33 -72.79 -71.71 13 B GLU 51 -65.27 -149.45 13 B ASP 52 -150.99 40.14 14 A PRO 256 -69.47 -141.77 14 A SER 277 -79.97 42.56 14 B GLN 2 -119.36 76.40 14 B THR 22 -71.92 -155.96 14 B GLN 62 -71.37 -144.20 14 B ARG 74 -75.58 -142.49 15 A SER 277 -179.39 136.94 15 B THR 9 -147.60 -48.99 15 B LEU 73 66.82 132.47 16 A ASN 276 -168.75 -43.30 16 A SER 277 -160.23 49.63 16 B THR 7 -92.96 -158.33 16 B THR 9 -76.38 34.91 16 B THR 22 -72.40 -153.15 16 B GLU 51 -67.12 -160.59 16 B ARG 72 -59.32 107.23 16 B LEU 73 47.44 -135.00 16 B ARG 74 -175.41 -42.57 17 A ASN 276 -172.92 135.42 17 A SER 277 -161.29 -44.48 17 B THR 7 -89.33 -152.80 17 B ARG 74 65.43 133.78 18 A ASN 276 66.04 135.74 18 A SER 277 63.85 129.62 18 B THR 7 -79.90 -151.44 18 B THR 9 -152.71 -43.11 18 B ALA 46 63.40 -72.84 18 B LEU 50 -77.31 38.45 18 B GLU 51 39.13 -144.58 18 B ASP 52 -168.46 36.91 18 B ARG 74 -173.05 -44.34 19 A ASN 276 -172.61 -43.52 19 A SER 277 -162.12 45.52 19 B THR 22 -70.13 -153.50 19 B LEU 50 -76.96 31.40 19 B GLU 51 43.16 -147.82 19 B ASP 52 -160.33 45.28 20 B THR 7 -88.28 -152.53 20 B THR 22 -74.64 -157.32 20 B GLU 51 -68.17 -155.38 20 B ASP 52 -123.21 -55.47 20 B LEU 73 53.72 -136.61 Solution structure of Vps27 amino-terminal UIM-ubiquitin complex 1 N N 2 N N A ASP 258 A ASP 4 HELX_P A GLU 273 A GLU 19 1 1 16 B THR 22 B THR 22 HELX_P B GLU 34 B GLU 34 5 2 13 B LEU 56 B LEU 56 HELX_P B TYR 59 B TYR 59 1 3 4 TRANSPORT PROTEIN PROTEIN-PROTEIN COMPLEX, TRANSPORT PROTEIN VPS27_YEAST UNP 1 256 P40343 TPEDEEELIRKAIELSLKESRNSA UBIQ_YEAST UNP 2 1 P61864 MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG 256 279 1Q0W 255 278 P40343 A 1 1 24 1 76 1Q0W 1 76 P61864 B 2 1 76 1 THR engineered mutation TYR 255 1Q0W A P40343 UNP 256 1 5 anti-parallel parallel anti-parallel anti-parallel B THR 12 B THR 12 B GLU 16 B GLU 16 B GLN 2 B GLN 2 B THR 7 B THR 7 B THR 66 B THR 66 B LEU 71 B LEU 71 B GLN 41 B GLN 41 B PHE 45 B PHE 45 B LYS 48 B LYS 48 B GLN 49 B GLN 49 1 P 1