1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kloks, C.P.A.M. Spronk, C.A.E.M. Hoffmann, A. Vuister, G.W. Grzesiek, S. Hilbers, C.W. 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 C11 H12 N2 O2 204.225 y TRYPTOPHAN 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 J.Mol.Biol. JMOBAK 0070 0022-2836 316 317 10.1006/JMBI.2001.5334 11851341 The Solution Structure and DNA-Binding Properties of the Cold-Shock Domain of the Human Y-Box Protein Yb-1. 2002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 SINGLE STRANDED DNA BINDING COLD SHOCK DOMAIN(CSD) OF HUMAN Y-BOX PROTEIN 1 (YB-1) 8754.899 Y-BOX BINDING PROTEIN COLD SHOCK DOMAIN 1 man polymer CSD no no MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG A 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 HUMAN sample 9606 HOMO SAPIENS 469008 ESCHERICHIA COLI BL21(DE3) PET11A repository Initial release Version format compliance Version format compliance 1 0 2002-02-21 1 1 2011-05-07 1 2 2011-07-13 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. PDBE Y PDBE 2001-02-23 REL THE SEQUENCE IS MATCHES TO SWISS PROT ENTRY Q90376 (RESIDUES 15-92) WHICH REPRESENTS Y-BOX BINDING PROTEIN FROM COLUMBA LIVIA (DOMESTIC PIGEON). N-TERMINAL METHIONINE ADDED IN PDB-SEQUENCE THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK DOMAIN OF HUMAN YB-1 10 10 15N-EDITED NOESY 15N-EDITED ROESY 13C-EDITED NOESY HNHA 0 6.7 pH 1 atm 303 K RESTRAINED MD TORSION ANGLE DYNAMICS FOLLOWED BY RESTRAINED MD 1 NILGES refinement MICHEAL NILGES X-PLOR X-PLOR X-PLOR structure solution NMRPIPE structure solution PIPP structure solution X-PLOR 500 Varian INOVA 600 Varian INOVA 750 Bruker DRX MET 1 n 1 MET 1 A LYS 2 n 2 LYS 2 A LYS 3 n 3 LYS 3 A VAL 4 n 4 VAL 4 A ILE 5 n 5 ILE 5 A ALA 6 n 6 ALA 6 A THR 7 n 7 THR 7 A LYS 8 n 8 LYS 8 A VAL 9 n 9 VAL 9 A LEU 10 n 10 LEU 10 A GLY 11 n 11 GLY 11 A THR 12 n 12 THR 12 A VAL 13 n 13 VAL 13 A LYS 14 n 14 LYS 14 A TRP 15 n 15 TRP 15 A PHE 16 n 16 PHE 16 A ASN 17 n 17 ASN 17 A VAL 18 n 18 VAL 18 A ARG 19 n 19 ARG 19 A ASN 20 n 20 ASN 20 A GLY 21 n 21 GLY 21 A TYR 22 n 22 TYR 22 A GLY 23 n 23 GLY 23 A PHE 24 n 24 PHE 24 A ILE 25 n 25 ILE 25 A ASN 26 n 26 ASN 26 A ARG 27 n 27 ARG 27 A ASN 28 n 28 ASN 28 A ASP 29 n 29 ASP 29 A THR 30 n 30 THR 30 A LYS 31 n 31 LYS 31 A GLU 32 n 32 GLU 32 A ASP 33 n 33 ASP 33 A VAL 34 n 34 VAL 34 A PHE 35 n 35 PHE 35 A VAL 36 n 36 VAL 36 A HIS 37 n 37 HIS 37 A GLN 38 n 38 GLN 38 A THR 39 n 39 THR 39 A ALA 40 n 40 ALA 40 A ILE 41 n 41 ILE 41 A LYS 42 n 42 LYS 42 A LYS 43 n 43 LYS 43 A ASN 44 n 44 ASN 44 A ASN 45 n 45 ASN 45 A PRO 46 n 46 PRO 46 A ARG 47 n 47 ARG 47 A LYS 48 n 48 LYS 48 A TYR 49 n 49 TYR 49 A LEU 50 n 50 LEU 50 A ARG 51 n 51 ARG 51 A SER 52 n 52 SER 52 A VAL 53 n 53 VAL 53 A GLY 54 n 54 GLY 54 A ASP 55 n 55 ASP 55 A GLY 56 n 56 GLY 56 A GLU 57 n 57 GLU 57 A THR 58 n 58 THR 58 A VAL 59 n 59 VAL 59 A GLU 60 n 60 GLU 60 A PHE 61 n 61 PHE 61 A ASP 62 n 62 ASP 62 A VAL 63 n 63 VAL 63 A VAL 64 n 64 VAL 64 A GLU 65 n 65 GLU 65 A GLY 66 n 66 GLY 66 A GLU 67 n 67 GLU 67 A LYS 68 n 68 LYS 68 A GLY 69 n 69 GLY 69 A ALA 70 n 70 ALA 70 A GLU 71 n 71 GLU 71 A ALA 72 n 72 ALA 72 A ALA 73 n 73 ALA 73 A ASN 74 n 74 ASN 74 A VAL 75 n 75 VAL 75 A THR 76 n 76 THR 76 A GLY 77 n 77 GLY 77 A PRO 78 n 78 PRO 78 A GLY 79 n 79 GLY 79 A author_defined_assembly 1 monomeric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N GLY 11 A N GLY 11 A O VAL 59 A O VAL 59 A N VAL 64 A N VAL 64 A O GLU 71 A O GLU 71 A N ALA 70 A N ALA 70 A O ASP 33 A O ASP 33 A N VAL 36 A N VAL 36 A O GLY 23 A O GLY 23 A N ASN 26 A N ASN 26 A O THR 12 A O THR 12 5 A A OE1 HZ3 GLU LYS 65 68 1.60 8 A A H3 OE1 MET GLU 1 32 1.55 3 A ARG 27 0.107 SIDE CHAIN 4 A ARG 27 0.108 SIDE CHAIN 4 A ARG 51 0.083 SIDE CHAIN 6 A ARG 27 0.080 SIDE CHAIN 7 A ARG 27 0.125 SIDE CHAIN 10 A ARG 19 0.086 SIDE CHAIN 1 3.45 0.50 120.30 123.75 A A A NE CZ NH1 ARG ARG ARG 27 27 27 N 2 3.26 0.50 120.30 123.56 A A A NE CZ NH1 ARG ARG ARG 51 51 51 N 3 3.62 0.50 120.30 123.92 A A A NE CZ NH1 ARG ARG ARG 19 19 19 N 3 4.22 0.50 120.30 124.52 A A A NE CZ NH1 ARG ARG ARG 27 27 27 N 7 -3.08 0.50 120.30 117.22 A A A NE CZ NH2 ARG ARG ARG 19 19 19 N 7 3.03 0.50 120.30 123.33 A A A NE CZ NH1 ARG ARG ARG 51 51 51 N 8 3.09 0.50 120.30 123.39 A A A NE CZ NH1 ARG ARG ARG 27 27 27 N 8 3.31 0.50 120.30 123.61 A A A NE CZ NH1 ARG ARG ARG 47 47 47 N 8 3.41 0.50 120.30 123.71 A A A NE CZ NH1 ARG ARG ARG 51 51 51 N 9 3.24 0.50 120.30 123.54 A A A NE CZ NH1 ARG ARG ARG 47 47 47 N 10 3.27 0.50 120.30 123.57 A A A NE CZ NH1 ARG ARG ARG 47 47 47 N 1 A LYS 3 -116.64 -98.61 1 A ILE 5 -91.37 -61.49 1 A TRP 15 37.11 63.67 1 A LYS 43 56.75 -118.54 1 A ARG 47 -112.19 60.07 1 A TYR 49 70.77 144.38 1 A LEU 50 -93.29 -81.30 1 A VAL 53 -128.27 -77.88 1 A GLU 67 -100.35 -71.23 1 A GLU 71 -122.37 -162.86 1 A THR 76 -96.32 -134.27 2 A ILE 5 -95.61 -72.87 2 A LYS 14 -100.32 -87.29 2 A LYS 42 65.34 -172.53 2 A ASN 44 53.21 -86.98 2 A LYS 48 66.74 -157.44 2 A GLU 67 -95.37 -136.61 2 A GLU 71 -107.01 -166.71 2 A THR 76 -125.96 -121.85 3 A LYS 2 -90.58 -76.52 3 A VAL 4 70.73 86.76 3 A ILE 5 -80.74 -72.08 3 A LYS 8 59.18 75.67 3 A ASN 17 -102.52 76.90 3 A ASN 28 -62.48 84.95 3 A ASP 29 -159.42 -76.12 3 A LYS 31 55.65 81.76 3 A LYS 48 59.32 -156.52 3 A LEU 50 -88.32 -143.21 3 A GLU 67 -78.30 -145.37 3 A GLU 71 -121.09 -168.10 3 A ASN 74 34.51 63.36 4 A LYS 8 53.38 83.01 4 A THR 30 -143.22 33.89 4 A TYR 49 -86.81 -147.64 4 A ARG 51 -139.71 -83.21 4 A GLU 67 -107.82 -89.57 4 A THR 76 -113.52 -122.09 5 A LYS 3 75.38 -98.90 5 A ASP 29 -76.25 -81.33 5 A LYS 31 77.57 62.29 5 A ASN 44 -76.73 -80.39 5 A TYR 49 66.32 159.74 5 A GLU 65 -139.95 -111.29 5 A GLU 67 -101.75 -69.78 6 A LYS 8 60.95 73.15 6 A LYS 14 -105.37 -86.95 6 A ASN 28 -82.54 48.00 6 A THR 30 -150.34 35.33 6 A LYS 31 57.87 75.99 6 A LYS 42 -73.43 -74.91 6 A TYR 49 -97.93 56.82 6 A ARG 51 -101.49 79.79 6 A SER 52 -107.02 -85.57 6 A VAL 53 -108.42 -106.58 6 A GLU 67 -123.67 -145.47 6 A GLU 71 -120.53 -168.04 6 A THR 76 -83.03 -82.85 7 A LYS 2 60.83 -72.20 7 A LYS 3 76.79 88.27 7 A VAL 4 -113.97 -72.54 7 A TRP 15 77.83 154.11 7 A ASP 29 -166.97 -76.56 7 A LYS 31 51.12 73.39 7 A ASN 44 69.53 -49.13 7 A LEU 50 -82.16 -86.83 7 A GLU 65 -144.26 -77.82 8 A LYS 3 -48.45 103.29 8 A VAL 4 61.90 103.64 8 A TRP 15 -69.83 -79.29 8 A PHE 16 75.10 114.69 8 A THR 30 -146.40 24.59 8 A LYS 31 67.09 76.37 8 A TYR 49 75.85 166.81 8 A ARG 51 71.40 112.76 8 A SER 52 -81.23 -70.37 8 A GLU 65 -160.25 -122.50 9 A LYS 3 -79.14 -97.16 9 A VAL 4 65.61 117.15 9 A LYS 14 -102.47 -99.14 9 A ARG 27 -36.12 147.65 9 A ASP 29 -82.94 -78.51 9 A LYS 31 60.09 67.53 9 A ASN 45 -118.53 68.58 9 A LYS 48 -92.50 -93.38 9 A LEU 50 74.20 -60.51 9 A ASP 55 66.71 -137.98 9 A GLU 67 -89.45 -136.23 9 A THR 76 -109.14 -158.53 10 A LYS 3 -145.78 -28.65 10 A LYS 8 59.06 73.12 10 A LYS 14 -95.14 -100.69 10 A ASP 29 -132.42 -72.57 10 A ARG 47 -107.54 -81.25 10 A GLU 65 -144.81 -60.30 10 A GLU 67 -80.12 -85.26 10 A GLU 71 -117.83 -166.81 10 A THR 76 -99.32 -103.39 Y-BOX BINDING PROTEIN Solution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures) 1 N N A THR 39 A THR 39 HELX_P A ILE 41 A ILE 41 5 1 3 TRANSLATION FACTOR TRANSLATION FACTOR, TRANSCRIPTION FACTOR, OB-FOLD, 5-STRANDED ANTI-PARALLEL BETA-BARREL, SINGLE STRANDED DNA BINDING, COLD SHOCK, Y-BOX 1H95 PDB 1 1H95 1 79 1H95 1 79 1H95 A 1 1 79 6 anti-parallel anti-parallel parallel anti-parallel anti-parallel A LYS 3 A LYS 3 A VAL 18 A VAL 18 A GLU 57 A GLU 57 A GLU 65 A GLU 65 A GLY 69 A GLY 69 A THR 76 A THR 76 A LYS 31 A LYS 31 A HIS 37 A HIS 37 A GLY 21 A GLY 21 A ASN 28 A ASN 28 A LYS 3 A LYS 3 A VAL 18 A VAL 18 1 P 1