14.40 12.601 -8.390 -1.212 A N ILE 1 ATOM A N ILE 1 1 1.00 1 N 14.86 11.409 -7.582 -1.598 A CA ILE 1 ATOM A CA ILE 1 1 1.00 1 C 15.15 11.447 -6.187 -1.019 A C ILE 1 ATOM A C ILE 1 1 1.00 1 C 15.28 11.624 -6.019 0.184 A O ILE 1 ATOM A O ILE 1 1 1.00 1 O 15.06 10.071 -8.190 -1.105 A CB ILE 1 ATOM A CB ILE 1 1 1.00 1 C 15.45 9.822 -9.555 -1.736 A CG1 ILE 1 ATOM A CG1 ILE 1 1 1.00 1 C 14.46 8.896 -7.243 -1.431 A CG2 ILE 1 ATOM A CG2 ILE 1 1 1.00 1 C 13.87 8.719 -10.338 -1.060 A CD1 ILE 1 ATOM A CD1 ILE 1 1 1.00 1 C 14.95 11.286 -5.195 -1.890 A N ILE 2 ATOM A N ILE 1 2 1.00 1 N 15.44 10.919 -3.862 -1.487 A CA ILE 2 ATOM A CA ILE 1 2 1.00 1 C 15.35 9.523 -3.593 -2.061 A C ILE 2 ATOM A C ILE 1 2 1.00 1 C 15.42 9.338 -3.591 -3.287 A O ILE 2 ATOM A O ILE 1 2 1.00 1 O 15.07 11.895 -2.801 -2.009 A CB ILE 2 ATOM A CB ILE 1 2 1.00 1 C 15.89 13.323 -3.103 -1.584 A CG1 ILE 2 ATOM A CG1 ILE 1 2 1.00 1 C 16.14 11.527 -1.437 -1.466 A CG2 ILE 2 ATOM A CG2 ILE 1 2 1.00 1 C 13.94 14.311 -2.022 -2.067 A CD1 ILE 2 ATOM A CD1 ILE 1 2 1.00 1 C 15.48 8.548 -3.384 -1.170 A N HIS 3 ATOM A N HIS 1 3 1.00 1 N 14.66 7.157 -3.199 -1.565 A CA HIS 3 ATOM A CA HIS 1 3 1.00 1 C 15.08 6.549 -1.944 -0.924 A C HIS 3 ATOM A C HIS 1 3 1.00 1 C 13.92 6.367 -1.847 0.298 A O HIS 3 ATOM A O HIS 1 3 1.00 1 O 14.83 6.331 -4.446 -1.229 A CB HIS 3 ATOM A CB HIS 1 3 1.00 1 C 12.74 4.904 -4.389 -1.700 A CG HIS 3 ATOM A CG HIS 1 3 1.00 1 C 11.28 3.916 -5.168 -1.144 A ND1 HIS 3 ATOM A ND1 HIS 1 3 1.00 1 N 12.74 4.297 -3.645 -2.653 A CD2 HIS 3 ATOM A CD2 HIS 1 3 1.00 1 C 10.42 2.764 -4.910 -1.730 A CE1 HIS 3 ATOM A CE1 HIS 1 3 1.00 1 C 10.20 2.961 -3.974 -2.640 A NE2 HIS 3 ATOM A NE2 HIS 1 3 1.00 1 N 14.93 6.233 -0.986 -1.787 A N PHE 4 ATOM A N PHE 1 4 1.00 1 N 15.32 5.578 0.242 -1.389 A CA PHE 4 ATOM A CA PHE 1 4 1.00 1 C 15.08 4.163 0.163 -1.949 A C PHE 4 ATOM A C PHE 1 4 1.00 1 C 15.04 3.922 0.469 -3.112 A O PHE 4 ATOM A O PHE 1 4 1.00 1 O 15.04 6.349 1.453 -1.920 A CB PHE 4 ATOM A CB PHE 1 4 1.00 1 C 17.30 7.510 1.860 -1.047 A CG PHE 4 ATOM A CG PHE 1 4 1.00 1 C 19.00 7.544 3.103 -0.443 A CD1 PHE 4 ATOM A CD1 PHE 1 4 1.00 1 C 17.85 8.553 0.994 -0.807 A CD2 PHE 4 ATOM A CD2 PHE 1 4 1.00 1 C 19.54 8.611 3.467 0.370 A CE1 PHE 4 ATOM A CE1 PHE 1 4 1.00 1 C 18.92 9.614 1.364 -0.001 A CE2 PHE 4 ATOM A CE2 PHE 1 4 1.00 1 C 17.54 9.641 2.596 0.582 A CZ PHE 4 ATOM A CZ PHE 1 4 1.00 1 C 15.28 3.245 -0.292 -1.113 A N GLY 5 ATOM A N GLY 1 5 1.00 1 N 15.77 1.874 -0.538 -1.541 A CA GLY 5 ATOM A CA GLY 1 5 1.00 1 C 16.20 1.277 -1.676 -0.760 A C GLY 5 ATOM A C GLY 1 5 1.00 1 C 16.34 1.748 -2.006 0.324 A O GLY 5 ATOM A O GLY 1 5 1.00 1 O 17.20 0.247 -2.298 -1.320 A N SER 6 ATOM A N SER 1 6 1.00 1 N 17.85 -0.488 -3.353 -0.621 A CA SER 6 ATOM A CA SER 1 6 1.00 1 C 18.85 -0.705 -4.607 -1.478 A C SER 6 ATOM A C SER 1 6 1.00 1 C 19.94 -0.263 -4.675 -2.638 A O SER 6 ATOM A O SER 1 6 1.00 1 O 17.78 -1.830 -2.804 -0.132 A CB SER 6 ATOM A CB SER 1 6 1.00 1 C 16.74 -1.621 -1.788 0.829 A OG SER 6 ATOM A OG SER 1 6 1.00 1 O 19.55 -1.319 -5.592 -1.029 A OXT SER 6 ATOM A OXT SER 1 6 1.00 1 O 52.17 4.495 -8.174 -1.940 A C1 MPD 7 HETATM B C1 MPD 2 1.00 1 C 51.81 4.360 -8.256 -3.445 A C2 MPD 7 HETATM B C2 MPD 2 1.00 1 C 51.08 3.776 -7.016 -3.921 A O2 MPD 7 HETATM B O2 MPD 2 1.00 1 O 51.56 5.759 -8.409 -4.028 A CM MPD 7 HETATM B CM MPD 2 1.00 1 C 52.22 3.501 -9.464 -3.828 A C3 MPD 7 HETATM B C3 MPD 2 1.00 1 C 52.51 1.977 -9.352 -3.653 A C4 MPD 7 HETATM B C4 MPD 2 1.00 1 C 52.98 1.528 -8.090 -3.199 A O4 MPD 7 HETATM B O4 MPD 2 1.00 1 O 52.46 1.281 -9.668 -4.976 A C5 MPD 7 HETATM B C5 MPD 2 1.00 1 C 0.036303 0.000000 0.000000 0.000000 0.032240 0.000000 0.000000 0.000000 0.208160 0.000000 0.000000 0.000000 Apostol, M.I. Sawaya, M.R. Eisenberg, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 27.546 31.017 4.804 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 H14 O2 118.174 (4S)-2-METHYL-2,4-PENTANEDIOL non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking N 1 N N N 2 N C N 3 N C N 4 N O N 5 N O N 6 N H N 7 N H N 8 N H N 9 N H N 10 N H N 11 N N N 12 S C N 13 N C N 14 N O N 15 N C Y 16 N C Y 17 N N Y 18 N C Y 19 N C Y 20 N N N 21 N O N 22 N H N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N N N 33 S C N 34 N C N 35 N O N 36 S C N 37 N C N 38 N C N 39 N C N 40 N O N 41 N H N 42 N H N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N C N 55 N C N 56 N O N 57 N C N 58 N C N 59 S C N 60 N O N 61 N C N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N N N 77 S C N 78 N C N 79 N O N 80 N C Y 81 N C Y 82 N C Y 83 N C Y 84 N C Y 85 N C Y 86 N C N 87 N O N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N N N 100 S C N 101 N C N 102 N O N 103 N C N 104 N O N 105 N O N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N doub N 17 N sing N 18 N sing N 19 N sing N 20 N sing Y 21 N sing Y 22 N doub Y 23 N doub N 24 N sing Y 25 N sing N 26 N sing Y 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N doub N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N doub N 80 N sing N 81 N sing N 82 N sing N 83 N sing Y 84 N doub Y 85 N sing Y 86 N sing N 87 N sing Y 88 N doub N 89 N sing Y 90 N doub N 91 N sing Y 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing US Biochemistry BICHAW 0033 0006-2960 50 2456 2463 10.1021/bi101803k 21323366 Atomic structures suggest determinants of transmission barriers in Mammalian prion disease. 2011 10.2210/pdb3nvf/pdb pdb_00003nvf 100 1 CCD 2008-01-01 MAR CCD 225 SINGLE WAVELENGTH M x-ray 1 0.8726 1.0 ID13 ESRF 0.8726 SYNCHROTRON ESRF BEAMLINE ID13 673.781 Major prion protein 1 syn polymer 118.174 (4S)-2-METHYL-2,4-PENTANEDIOL 1 syn non-polymer PrP, PrP27-30, PrP33-35C, ASCR no no IIHFGS IIHFGS A polypeptide(L) n n n n n n 1 1.52 19.23 VAPOR DIFFUSION, HANGING DROP 7.4 100mM Tris pH 7.4, 25% MPD, vapor diffusion, hanging drop, temperature 298K 298 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Data collection Database references Derived calculations 1 0 2011-03-02 1 1 2011-07-13 1 2 2024-02-21 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id MMHFGN hexapeptide (residues 138-143) from golden hamster prion protein MIHFGN hexapeptide (residues 137-142) from mouse prion protein MIHFGND (residues 137-143) from mouse prion protein RCSB Y RCSB 2010-07-08 REL REL MPD (4S)-2-METHYL-2,4-PENTANEDIOL IIHFGS (UNP residues 138-143) from human prion 9606 human Homo sapiens sample MPD 1 2 MPD MPD 7 A 2.200 2.200 20.600 20.600 Phaser MODE: MR_AUTO ILE 1 n 1 ILE 1 A ILE 2 n 2 ILE 2 A HIS 3 n 3 HIS 3 A PHE 4 n 4 PHE 4 A GLY 5 n 5 GLY 5 A SER 6 n 6 SER 6 A author_defined_assembly 10 decameric 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 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_557 x,y,z+2 crystal symmetry operation 0.0000000000 0.0000000000 9.6080000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_556 x,y,z+1 crystal symmetry operation 0.0000000000 0.0000000000 4.8040000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_554 x,y,z-1 crystal symmetry operation 0.0000000000 0.0000000000 -4.8040000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_553 x,y,z-2 crystal symmetry operation 0.0000000000 0.0000000000 -9.6080000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_657 -x+1,-y,z+2 crystal symmetry operation 27.5460000000 0.0000000000 9.6080000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_656 -x+1,-y,z+1 crystal symmetry operation 27.5460000000 0.0000000000 4.8040000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_655 -x+1,-y,z crystal symmetry operation 27.5460000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_654 -x+1,-y,z-1 crystal symmetry operation 27.5460000000 0.0000000000 -4.8040000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 2_653 -x+1,-y,z-2 crystal symmetry operation 27.5460000000 0.0000000000 -9.6080000000 52.980 20.8202 10.200 1.0000 0.0000 0.0000 -0.0400 0.0000 -0.9500 0.9550 0.9400 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.2263 0.2118 0.2133 1.8000 20.6000 40 433 9.2000 86.4300 0.2521 0.2013 1.000 1.000 0.8682 4.0090 0.1110 0.2379 0.1668 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.1670 0.8000 0.8000 1.4000 MAXIMUM LIKELIHOOD MASK 1.8000 20.6000 0 56 8 0 48 0.009 0.021 56 0.001 0.020 35 1.657 2.043 75 0.693 3.000 84 9.100 5.000 5 52.201 20.000 2 10.817 15.000 7 0.053 0.200 8 0.004 0.020 52 0.001 0.020 12 0.523 1.500 29 0.157 1.500 12 0.853 2.000 46 1.220 3.000 27 1.673 4.500 29 0.3300 0.3820 2.0110 4 87 91 5 72.2200 1.800 90.000 3NVF 443 0.216 1.137 1 6.800 3.800 85.400 0.395 1.800 1.940 63 1.424 1.700 67.000 0.327 1.940 2.130 83 1.294 2.300 85.600 0.314 2.130 2.440 89 0.964 3.200 78.800 0.244 2.440 3.080 87 1.062 5.400 100.000 0.197 3.080 90.000 121 1.199 5.100 94.500 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO program data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK program phasing Randy J. Read cimr-phaser@lists.cam.ac.uk Wed Feb 15 11:59:26 2006 http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program 1.3.2 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 IIHFGS segment 138-143 from human prion 1 N N 2 N N PROTEIN FIBRIL amyloid-like protofibril, PROTEIN FIBRIL PRIO_HUMAN UNP 1 138 P04156 IIHFGS 138 143 3NVF 1 6 P04156 A 1 1 6 BINDING SITE FOR RESIDUE MPD A 7 A MPD 7 Software 5 A ILE 1 A ILE 1 5 4_444 A ILE 2 A ILE 2 5 4_444 A HIS 3 A HIS 3 5 1_555 A HIS 3 A HIS 3 5 1_554 A PHE 4 A PHE 4 5 3_544 18 P 21 21 2