11.67 3.411 1.437 1.677 A N ASN 1 ATOM A N ASN 1 1 1.00 1 N 10.39 4.238 1.323 2.910 A CA ASN 1 ATOM A CA ASN 1 1 1.00 1 C 5.67 3.458 1.873 4.113 A C ASN 1 ATOM A C ASN 1 1 1.00 1 C 8.67 3.204 3.072 4.184 A O ASN 1 ATOM A O ASN 1 1 1.00 1 O 11.66 5.548 2.119 2.748 A CB ASN 1 ATOM A CB ASN 1 1 1.00 1 C 25.39 6.605 1.424 1.878 A CG ASN 1 ATOM A CG ASN 1 1 1.00 1 C 10.94 6.671 0.207 1.798 A OD1 ASN 1 ATOM A OD1 ASN 1 1 1.00 1 O 15.31 7.486 2.229 1.270 A ND2 ASN 1 ATOM A ND2 ASN 1 1 1.00 1 N 9.62 3.063 0.982 5.021 A N ASN 2 ATOM A N ASN 1 2 1.00 1 N 6.92 2.425 1.353 6.293 A CA ASN 2 ATOM A CA ASN 1 2 1.00 1 C 8.06 3.326 0.815 7.400 A C ASN 2 ATOM A C ASN 1 2 1.00 1 C 8.46 3.599 -0.368 7.434 A O ASN 2 ATOM A O ASN 1 2 1.00 1 O 5.26 1.055 0.680 6.469 A CB ASN 2 ATOM A CB ASN 1 2 1.00 1 C 5.77 -0.071 1.341 5.711 A CG ASN 2 ATOM A CG ASN 1 2 1.00 1 C 9.71 -0.112 2.558 5.522 A OD1 ASN 2 ATOM A OD1 ASN 1 2 1.00 1 O 7.31 -1.038 0.528 5.313 A ND2 ASN 2 ATOM A ND2 ASN 1 2 1.00 1 N 9.80 3.742 1.682 8.319 A N GLN 3 ATOM A N GLN 1 3 1.00 1 N 8.25 4.661 1.318 9.397 A CA GLN 3 ATOM A CA GLN 1 3 1.00 1 C 7.42 4.192 1.934 10.703 A C GLN 3 ATOM A C GLN 1 3 1.00 1 C 7.60 3.929 3.129 10.771 A O GLN 3 ATOM A O GLN 1 3 1.00 1 O 8.03 6.069 1.806 9.050 A CB GLN 3 ATOM A CB GLN 1 3 1.00 1 C 11.30 7.161 1.427 10.051 A CG GLN 3 ATOM A CG GLN 1 3 1.00 1 C 13.08 8.510 2.005 9.664 A CD GLN 3 ATOM A CD GLN 1 3 1.00 1 C 10.87 8.723 3.220 9.721 A OE1 GLN 3 ATOM A OE1 GLN 1 3 1.00 1 O 8.58 9.431 1.135 9.256 A NE2 GLN 3 ATOM A NE2 GLN 1 3 1.00 1 N 10.51 4.065 1.109 11.740 A N GLN 4 ATOM A N GLN 1 4 1.00 1 N 13.23 3.653 1.603 13.060 A CA GLN 4 ATOM A CA GLN 1 4 1.00 1 C 17.04 4.267 0.783 14.189 A C GLN 4 ATOM A C GLN 1 4 1.00 1 C 10.73 4.912 -0.221 13.917 A O GLN 4 ATOM A O GLN 1 4 1.00 1 O 13.91 2.133 1.601 13.170 A CB GLN 4 ATOM A CB GLN 1 4 1.00 1 C 12.46 1.523 0.225 13.111 A CG GLN 4 ATOM A CG GLN 1 4 1.00 1 C 18.51 -0.002 0.229 13.199 A CD GLN 4 ATOM A CD GLN 1 4 1.00 1 C 15.35 -0.614 -0.835 13.240 A OE1 GLN 4 ATOM A OE1 GLN 1 4 1.00 1 O 19.68 -0.617 1.419 13.241 A NE2 GLN 4 ATOM A NE2 GLN 1 4 1.00 1 N 7.44 4.133 1.082 15.384 A OXT GLN 4 ATOM A OXT GLN 1 4 1.00 1 O 0.1082 0.0331 -0.0340 0.2008 -0.0062 0.1343 A N ASN 1 A N ASN 1 N 0.1106 0.0673 0.0441 0.1428 -0.0464 0.1410 A CA ASN 1 A CA ASN 1 C 0.1189 -0.0062 0.0221 0.0831 -0.0081 0.0132 A C ASN 1 A C ASN 1 C 0.1419 0.0077 0.0163 0.1151 0.0271 0.0723 A O ASN 1 A O ASN 1 O 0.1599 -0.0228 0.0232 0.1305 -0.0446 0.1524 A CB ASN 1 A CB ASN 1 C 0.3190 -0.0525 -0.0093 0.2554 0.0466 0.3900 A CG ASN 1 A CG ASN 1 C 0.1173 0.0066 0.0354 0.1659 0.0105 0.1324 A OD1 ASN 1 A OD1 ASN 1 O 0.1895 0.0926 0.0669 0.1031 -0.0044 0.2890 A ND2 ASN 1 A ND2 ASN 1 N 0.1228 0.0041 -0.0377 0.1350 -0.0177 0.1075 A N ASN 2 A N ASN 2 N 0.1062 0.0383 0.0052 0.1339 0.0246 0.0225 A CA ASN 2 A CA ASN 2 C 0.1062 0.0007 -0.0076 0.1182 0.0023 0.0818 A C ASN 2 A C ASN 2 C 0.1587 0.0182 -0.0174 0.1011 -0.0164 0.0613 A O ASN 2 A O ASN 2 O 0.1066 0.0265 0.0064 0.0895 0.0035 0.0036 A CB ASN 2 A CB ASN 2 C 0.0993 -0.0055 0.0184 0.0967 -0.0314 0.0230 A CG ASN 2 A CG ASN 2 C 0.1628 -0.0335 -0.0465 0.1280 0.0075 0.0778 A OD1 ASN 2 A OD1 ASN 2 O 0.1323 -0.0061 0.0090 0.1066 0.0282 0.0388 A ND2 ASN 2 A ND2 ASN 2 N 0.1227 0.0143 -0.0106 0.1427 -0.0419 0.1068 A N GLN 3 A N GLN 3 N 0.1307 0.0500 0.0260 0.1068 -0.0032 0.0759 A CA GLN 3 A CA GLN 3 C 0.1441 0.0122 -0.0355 0.0781 0.0093 0.0594 A C GLN 3 A C GLN 3 C 0.1130 0.0087 -0.0006 0.1085 0.0157 0.0671 A O GLN 3 A O GLN 3 O 0.0927 0.0547 -0.0058 0.1396 -0.0540 0.0726 A CB GLN 3 A CB GLN 3 C 0.1391 -0.0104 0.0126 0.1940 0.0318 0.0962 A CG GLN 3 A CG GLN 3 C 0.1852 -0.0225 -0.0079 0.1665 -0.0106 0.1450 A CD GLN 3 A CD GLN 3 C 0.1586 -0.0223 -0.0177 0.1594 -0.0251 0.0947 A OE1 GLN 3 A OE1 GLN 3 O 0.1061 0.0308 -0.0111 0.1277 -0.0086 0.0919 A NE2 GLN 3 A NE2 GLN 3 N 0.1391 0.0161 0.0288 0.1154 0.0345 0.1446 A N GLN 4 A N GLN 4 N 0.2064 -0.0095 0.0424 0.1613 -0.0216 0.1350 A CA GLN 4 A CA GLN 4 C 0.2070 -0.0391 0.0409 0.1928 0.0257 0.2475 A C GLN 4 A C GLN 4 C 0.1486 0.0114 0.0145 0.1510 0.0015 0.1081 A O GLN 4 A O GLN 4 O 0.1725 -0.0002 0.0141 0.2043 -0.0138 0.1515 A CB GLN 4 A CB GLN 4 C 0.1039 -0.0292 -0.0175 0.1866 0.0253 0.1830 A CG GLN 4 A CG GLN 4 C 0.1501 0.0424 -0.0632 0.1590 -0.0426 0.3940 A CD GLN 4 A CD GLN 4 C 0.1529 0.0291 -0.0237 0.2418 0.0098 0.1883 A OE1 GLN 4 A OE1 GLN 4 O 0.1877 -0.0390 0.0359 0.2023 0.0085 0.3576 A NE2 GLN 4 A NE2 GLN 4 N 0.1041 0.0013 -0.0137 0.0954 0.0003 0.0830 A OXT GLN 4 A OXT GLN 4 O 0.064604 0.000000 0.000000 0.000000 0.203459 0.000000 0.000000 0.000000 0.032731 0.000000 0.000000 0.000000 Nelson, R. Sawaya, M.R. Eisenberg, D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 15.479 4.915 30.552 C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N C N 7 N O N 8 N N N 9 N O N 10 N H N 11 N H N 12 N H N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N N N 19 S C N 20 N C N 21 N O N 22 N C N 23 N C N 24 N C N 25 N O N 26 N N N 27 N O N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 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 doub N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N doub N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N sing N 33 N sing N 34 N sing N 35 N sing UK Nature NATUAS 0006 0028-0836 447 453 457 10.1038/nature05695 17468747 Atomic structures of amyloid cross-beta spines reveal varied steric zippers. 2007 10.2210/pdb2olx/pdb pdb_00002olx 100 1 CCD 2005-12-19 MAR CCD 165 mm SINGLE WAVELENGTH M x-ray 1 0.94660 1.0 ID13 ESRF 0.94660 SYNCHROTRON ESRF BEAMLINE ID13 502.478 NNQQ peptide derived from Yeast Prion Sup35 residues 8-11 1 syn polymer no no NNQQ NNQQ A polypeptide(L) n n n n 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Refinement description Data collection Database references Refinement description 1 0 2007-01-30 1 1 2008-05-01 1 2 2011-07-13 1 3 2017-10-18 1 4 2023-12-27 1 5 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession RCSB Y RCSB 2007-01-19 REL REL polyalanine ideal beta-strand Other in silico model ASN 1 n 1 ASN 1 A ASN 2 n 2 ASN 2 A GLN 3 n 3 GLN 3 A GLN 4 n 4 GLN 4 A author_defined_assembly 3 trimeric 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_565 x,y+1,z crystal symmetry operation 0.0000000000 4.9150000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3_555 -x,y+1/2,-z+1/2 crystal symmetry operation 0.0000000000 2.4575000000 15.2760000000 8.984 -1.110 0.000 0.000 -0.850 0.000 1.950 0.961 0.971 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.235 0.183 0.188 1.420 15.280 39 426 413 9.400 74.280 1.750 0.033 RANDOM 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.229 0.117 0.800 0.800 1.400 polyalanine ideal beta-strand MAXIMUM LIKELIHOOD MASK 1.420 15.280 0 35 0 0 35 0.008 0.021 34 0.001 0.020 19 1.397 1.851 45 0.615 3.000 48 4.135 5.000 3 40.192 30.000 4 10.806 15.000 6 0.166 0.200 4 0.005 0.020 41 0.000 0.020 3 0.180 0.200 13 0.133 0.200 13 0.079 0.200 16 0.137 0.200 10 0.108 0.200 1 6.472 2.000 28 3.013 2.000 7 6.638 3.000 31 9.714 2.000 14 7.745 3.000 14 6.143 3.000 61 6.513 3.000 54 0.267 0.237 1.456 3 14 17 20 45.950 18.8 1.400 90.000 2OLX 426 426 -3 0.124 1.072 1 8.700 3.100 74.900 0.209 1.40 1.45 25 0.900 2.80 54.30 0.199 1.45 1.51 34 1.095 2.60 59.60 0.144 1.51 1.58 27 1.140 2.60 46.60 0.139 1.58 1.66 27 1.078 2.70 44.30 0.121 1.66 1.76 31 1.146 2.60 66.00 0.139 1.76 1.90 46 0.999 3.20 95.80 0.153 1.90 2.09 51 1.102 3.10 94.40 0.148 2.09 2.39 60 0.989 3.30 90.90 0.124 2.39 3.02 52 1.028 3.90 91.20 0.097 3.02 90.00 73 1.212 3.00 97.30 data reduction Zbyszek Otwinowski zbyszek@mix.swmed.edu http://www.lnls.br/infra/linhasluz/denzo-hkl.htm DENZO package data scaling Zbyszek Otwinowski zbyszek@mix.swmed.edu http://www.lnls.br/infra/linhasluz/denzo-hkl.htm SCALEPACK package phasing R. J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER other refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran_77 http://www.ccp4.ac.uk/main.html REFMAC program data extraction PDB sw-help@rcsb.rutgers.edu April. 3, 2006 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 2.000 Structure of NNQQ Peptide from Yeast Prion SUP35 1 N N One sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X,1/2+Y,1/2-Z, and repeated unit cell translations of this strand along the b axis. PROTEIN FIBRIL steric zipper, glutamine zipper, polar zipper, asparagine zipper, PROTEIN FIBRIL 2OLX PDB 1 2OLX 1 4 2OLX 1 4 2OLX A 1 1 4 19 P 21 21 21