0.034247 0.000000 0.007215 0.000000 0.205339 0.000000 0.000000 0.000000 0.031503 0.000000 0.000000 0.000000 0000-0003-0874-9043 Sawaya, M.R. 0000-0002-9612-0511 Warmack, R.A. 0000-0002-4487-0230 Boyer, D.R. 0000-0002-6630-706X Zee, C.T. 0000-0002-1694-1652 Richards, L.S. 0000-0002-3877-6803 Cascio, D. 0000-0002-9254-4069 Gonen, T. 0000-0002-7303-6632 Clarke, S.G. 0000-0003-2432-5419 Eisenberg, D.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.000 101.900 90.000 29.200 4.870 32.440 C3 H7 N O2 89.093 y ALANINE 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 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C4 H7 N O4 133.103 BETA-L-ASPARTIC ACID L-aspartic acid L-beta-peptide, C-gamma 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 C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Nat Commun 2041-1723 10 3357 3357 10.1038/s41467-019-11183-z 31350392 Structure of amyloid-beta (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface. 2019 0000-0002-9612-0511 0000-0003-0874-9043 0000-0001-8285-754X 0000-0002-9254-4069 0000-0003-2432-5419 10.2210/pdb6nb9/pdb pdb_00006nb9 100 1 CMOS CAMERA 2018-04-13 CETA 16M 0.0251 1.0 0.0251 ELECTRON MICROSCOPE TALOS ARCTICA 90.000 101.897 90.000 29.20 4.87 32.44 P 21 4 10.135 OTHER RECIPROCAL maximum liklihood 6NB9 DIFFRACTION PATTERN/LAYERLINES 3D CRYSTAL 7.6 water 1 1 NONE 1050 1 1 41.2 1.00 1.05 3.09 315 0.1 82.7 1.05 1 16529 3946 28.4 0.1 0.1 0.197 0.197 1 crystal of amyloid-beta residues 20-34 with L-isoaspartate at position 23 0 MULTIPLE SOURCES COMPLEX NO KILODALTONS/NANOMETER 6.21 3D ARRAY 1 1 CRYSTALLOGRAPHY 3 0.01 FEI CETA (4k x 4k) 159 2 2048 2048 6NB9 200 BASIC NITROGEN FIELD EMISSION GUN FLOOD BEAM FEI TALOS ARCTICA DIFFRACTION 100 100 FEI TITAN KRIOS AUTOGRID HOLDER 1 COPPER 300 Quantifoil R1.2/1.3 IMAGE ACQUISITION 1 MASKING CTF CORRECTION 1 LAYERLINE INDEXING DIFFRACTION INDEXING MODEL FITTING 1 Coot 0.8.9.1 OTHER MOLECULAR REPLACEMENT 1 LATTICE DISTORTION CORRECTION 1 SYMMETRY DETERMINATION 1 CRYSTALLOGRAPHY MERGING 1 RECONSTRUCTION 1 MODEL REFINEMENT 1 PHENIX 1.14-3260 2.5 This sample is a crystal. NO NO NO YES 100 ETHANE 6NB9 FEI VITROBOT MARK IV 1491.666 Amyloid-beta A4 protein residues 20-34 L-isoaspartate 23 1 syn polymer 18.015 water 4 nat water ABPP,APPI,APP,Alzheimer disease amyloid protein,Amyloid precursor protein,Amyloid-beta precursor protein,Cerebral vascular amyloid peptide,CVAP,PreA4,Protease nexin-II,PN-II no yes FAE(IAS)VGSNKGAIIGL FAEDVGSNKGAIIGL A polypeptide(L) n n n n n n n n n n n n n n n 1.51 18.76 BATCH 7.6 0.05M Tris-HCl, 0.15M NaCl, 1% DMSO 310 pdbx_audit_support database_2 em_diffraction_shell refine_hist repository Initial release Author supporting evidence Data collection Database references Refinement description 1 0 2019-08-07 1 1 2019-11-20 1 2 2022-09-07 _pdbx_audit_support.funding_organization _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_diffraction_shell.em_diffraction_stats_id _em_diffraction_shell.id _refine_hist.pdbx_refine_id United States National Institutes of Health/National Center for Research Resources (NIH/NCRR) 5T32GM008496 United States National Science Foundation (NSF, United States) MCB-1714569 United States National Institutes of Health/National Center for Research Resources (NIH/NCRR) GM-007185 United States Howard Hughes Medical Institute (HHMI) Amyloid-Beta (20-34) with L-isoaspartate 23 N RCSB Y RCSB 2018-12-06 REL REL HOH water human 9606 Human Homo sapiens sample 1 15 HOH 3 2 HOH HOH 101 A HOH 4 2 HOH HOH 102 A HOH 1 2 HOH HOH 103 A HOH 2 2 HOH HOH 104 A PHE 20 n 1 PHE 20 A ALA 21 n 2 ALA 21 A GLU 22 n 3 GLU 22 A ASI 23 n 4 IAS 23 A VAL 24 n 5 VAL 24 A GLY 25 n 6 GLY 25 A SER 26 n 7 SER 26 A ASN 27 n 8 ASN 27 A LYS 28 n 9 LYS 28 A GLY 29 n 10 GLY 29 A ALA 30 n 11 ALA 30 A ILE 31 n 12 ILE 31 A ILE 32 n 13 ILE 32 A GLY 33 n 14 GLY 33 A LEU 34 n 15 LEU 34 A author_defined_assembly 10 decameric microscopy 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_545 x,y-1,z crystal symmetry operation 0.0000000000 -4.8700000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_535 x,y-2,z crystal symmetry operation 0.0000000000 -9.7400000000 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 4.8700000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_575 x,y+2,z crystal symmetry operation 0.0000000000 9.7400000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_555 -x,y+1/2,-z crystal symmetry operation 0.0000000000 2.4350000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_545 -x,y-1/2,-z crystal symmetry operation 0.0000000000 -2.4350000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_535 -x,y-3/2,-z crystal symmetry operation 0.0000000000 -7.3050000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_565 -x,y+3/2,-z crystal symmetry operation 0.0000000000 7.3050000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_575 -x,y+5/2,-z crystal symmetry operation 0.0000000000 12.1750000000 0.0000000000 34.450 10.1351 3.360 0.2458 0.1976 0.2022 1.0500 5.9550 394 3943 9.9900 83.4500 0.1000 Random 1 THROUGHOUT 1.360 AB INITIO PHASING 28.4000 0.9000 1.1100 1.0500 5.9550 4 109 27.22 0 0 105 15 0.3257 0.0000 0.2697 1.2010 116 1051 1167 3 75.0000 0.2482 0.0000 0.2373 1.5090 134 1206 1340 3 89.0000 0.2233 0.0000 0.1676 5.9546 144 1292 1436 3 86.0000 9.691 1.050 5.955 6NB9 3946 0.984 0.197 0.224 0.888 1 3.760 16529 4.189 16 82.700 0.494 1.050 1.100 1.400 974 594 315 0.779 0.589 1 3.092 53.000 0.603 1.100 1.150 1.690 1794 511 452 0.661 0.690 1 3.969 88.500 0.509 1.150 1.200 2.210 2024 443 392 0.661 0.570 1 5.163 88.500 0.413 1.200 1.300 2.430 2436 645 567 0.832 0.471 1 4.296 87.900 0.347 1.300 1.400 2.800 1630 469 424 0.876 0.403 1 3.844 90.400 0.330 1.400 1.500 3.380 1432 376 333 0.851 0.378 1 4.300 88.600 0.219 1.500 2.000 5.410 3712 943 832 0.952 0.246 1 4.462 88.200 0.159 2.000 3.000 7.320 1853 529 450 0.975 0.182 1 4.118 85.100 0.129 3.000 5.000 7.660 650 201 171 0.980 0.145 1 3.801 85.100 0.076 5.000 5.955 5.920 22 58 10 0.989 0.105 1 2.200 17.200 data reduction Wolfgang Kabsch Wolfgang.Kabsch@mpimf-heidelberg.mpg.de http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ XDS package data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package data extraction PDB deposit@deposit.rcsb.org Sep. 1, 2017 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.24 phasing SHELXDE N Protofilament structure of Amyloid-beta 20-34 with the age-associated post-translational modification of aspartate isomerization at position 23 Amyloid-Beta (20-34) with L-isoaspartate 23 1 N N 2 N N covale 1.344 both A GLU 22 A C GLU 3 1_555 A IAS 23 A N IAS 4 1_555 covale 1.328 both A IAS 23 A CG IAS 4 1_555 A VAL 24 A N VAL 5 1_555 PROTEIN FIBRIL protofilament, 2 sub 1 screw symmetry, post-translational modification, isoaspartate, PROTEIN FIBRIL A4_HUMAN UNP 1 691 P05067 FAEDVGSNKGAIIGL 691 705 6NB9 20 34 P05067 A 1 1 15 1 ASP engineered mutation IAS 23 6NB9 A P05067 UNP 694 4 4 P 1 21 1