1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Schmidt, M. Rohou, A. Lasker, K. Yadav, J.K. Schiene-Fischer, C. Fandrich, M. Grigorieff, N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.0 90.0 90.0 1.0 1.0 1.0 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 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 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 C3 H7 N O3 105.093 y SERINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 112 11858 10.1073/PNAS.1503455112 26351699 Peptide Dimer Structure in an Abeta(1-42) Fibril Visualized with Cryo-Em 2015 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 METHOD--DIREX REFINEMENT PROTOCOL--PEPTIDE CHAIN OTHER REAL ELECTRON DENSITY 1.2 FINAL MAP WAS CALCULATED FROM 29 SINGLE FILAMENT RECONSTRUCTIONS. DATA USED FOR REFINEMENT WAS NEVER BELOW 10 ANGSTROM RESOLUTION. RESOLUTION OF FIBRIL CORE IS ABOUT 5 ANGSTROM. 3 POSSIBLE MODELS FOR THE CENTRAL REGION OF A ABETA(1-42) FIBRIL RECONSTRUCTION. MODEL1 ABETA(17-42) MODEL2 ABETA( 16-41) MODEL3 ABETA(15-40) SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3132. (DEPOSITION ID: 13698). 5AEF PROJECTION MATCHING AND FOURIER INVERSION 62320 5 HELICAL 50MM TRIS-HCL 50MM TRIS-HCL 7.4 INDIVIDUAL HELICAL SUBUNITS FIBRIL ABETA(1-42) AMYLOID-LIKE FIBRIL 0 COMPLEX FILAMENT 1 1 HELICAL 30 KODAK SO-163 FILM 5AEF 29 300 58333 2010-02-05 FIELD EMISSION GUN FLOOD BEAM FEI TECNAI F30 BRIGHT FIELD 2.0 3000 1750 59000 1 100 HOLEY CARBON RECONSTRUCTION 1 FREALIX 1 NO NO NO YES ETHANE 4 SEC BACKSIDE BLOTTING 5AEF GATAN CRYOPLUNGE 3 2835.365 AMYLOID BETA A4 PROTEIN ABETA, UNP RESIDUES 630-657 2 syn polymer ABETA17-42 no no QKLVFFAEDVGSNKGAIIGLMVGGVVIA QKLVFFAEDVGSNKGAIIGLMVGGVVIA A,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 pdbx_validate_polymer_linkage em_software atom_sites cell cell repository Initial release Database references Advisory Data collection Data collection Other Data collection Other 1 0 2015-10-14 1 1 2015-10-21 1 2 2017-08-30 1 3 2018-10-03 1 4 2019-10-02 1 5 2019-10-23 _pdbx_validate_polymer_linkage.dist _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.label_alt_id_2 _em_software.image_processing_id _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] _cell.length_a _cell.length_b _cell.length_c _cell.Z_PDB SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 3-STRANDED BARREL THIS IS REPRESENTED BY A 4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. PDBE Y PDBE 2015-08-29 REL 9606 HUMAN HOMO SAPIENS sample GLN 15 n 1 GLN 15 A LYS 16 n 2 LYS 16 A LEU 17 n 3 LEU 17 A VAL 18 n 4 VAL 18 A PHE 19 n 5 PHE 19 A PHE 20 n 6 PHE 20 A ALA 21 n 7 ALA 21 A GLU 22 n 8 GLU 22 A ASP 23 n 9 ASP 23 A VAL 24 n 10 VAL 24 A GLY 25 n 11 GLY 25 A SER 26 n 12 SER 26 A ASN 27 n 13 ASN 27 A LYS 28 n 14 LYS 28 A GLY 29 n 15 GLY 29 A ALA 30 n 16 ALA 30 A ILE 31 n 17 ILE 31 A ILE 32 n 18 ILE 32 A GLY 33 n 19 GLY 33 A LEU 34 n 20 LEU 34 A MET 35 n 21 MET 35 A VAL 36 n 22 VAL 36 A GLY 37 n 23 GLY 37 A GLY 38 n 24 GLY 38 A VAL 39 n 25 VAL 39 A VAL 40 n 26 VAL 40 A ILE 41 n 27 ILE 41 A ALA 42 n 28 ALA 42 A GLN 15 n 1 GLN 15 B LYS 16 n 2 LYS 16 B LEU 17 n 3 LEU 17 B VAL 18 n 4 VAL 18 B PHE 19 n 5 PHE 19 B PHE 20 n 6 PHE 20 B ALA 21 n 7 ALA 21 B GLU 22 n 8 GLU 22 B ASP 23 n 9 ASP 23 B VAL 24 n 10 VAL 24 B GLY 25 n 11 GLY 25 B SER 26 n 12 SER 26 B ASN 27 n 13 ASN 27 B LYS 28 n 14 LYS 28 B GLY 29 n 15 GLY 29 B ALA 30 n 16 ALA 30 B ILE 31 n 17 ILE 31 B ILE 32 n 18 ILE 32 B GLY 33 n 19 GLY 33 B LEU 34 n 20 LEU 34 B MET 35 n 21 MET 35 B VAL 36 n 22 VAL 36 B GLY 37 n 23 GLY 37 B GLY 38 n 24 GLY 38 B VAL 39 n 25 VAL 39 B VAL 40 n 26 VAL 40 B ILE 41 n 27 ILE 41 B ALA 42 n 28 ALA 42 B software_defined_assembly PISA 2 dimeric 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 LEU 17 A N LEU 3 A O LEU 17 A O LEU 3 A N LEU 34 A N LEU 20 A O GLY 33 A O GLY 19 A N ILE 31 A N ILE 17 A O ALA 30 A O ALA 16 A N VAL 36 A N VAL 22 A O MET 35 A O MET 21 B N LEU 17 B N LEU 3 B O LEU 17 B O LEU 3 B N PHE 19 B N PHE 5 B O PHE 19 B O PHE 5 B N PHE 19 B N PHE 5 B O LEU 17 B O LEU 3 B N LYS 28 B N LYS 14 B O ASN 27 B O ASN 13 B N ILE 32 B N ILE 18 B O ILE 31 B O ILE 17 B N MET 35 B N MET 21 B O MET 35 B O MET 21 B N LYS 28 B N LYS 14 B O ASN 27 B O ASN 13 B N GLY 33 B N GLY 19 B O ILE 32 B O ILE 18 B N MET 35 B N MET 21 B O MET 35 B O MET 21 B N LYS 28 B N LYS 14 B O ASN 27 B O ASN 13 B N LYS 28 B N LYS 14 B O ASN 27 B O ASN 13 1 A CD1 ILE 31 A CD1 ILE 17 1 Y 1 A CD1 ILE 32 A CD1 ILE 18 1 Y 1 A CD1 ILE 41 A CD1 ILE 27 1 Y 1 A O ALA 42 A O ALA 28 1 Y 1 B CD1 ILE 31 B CD1 ILE 17 1 Y 1 B CD1 ILE 32 B CD1 ILE 18 1 Y 1 B CD1 ILE 41 B CD1 ILE 27 1 Y 1 B O ALA 42 B O ALA 28 1 Y 1 A A C N GLN LEU 15 17 0.59 B 1 B B C CD1 GLN LEU 15 17 0.64 C 1 A A O C VAL ALA 39 42 0.67 A 1 A A C C VAL ALA 39 42 0.79 A 1 B B C N GLN LEU 15 17 0.80 B 1 B B CG2 CB ILE ALA 41 42 0.83 A 1 A A N N VAL ALA 39 42 0.98 A 1 B B CG2 CA ILE ALA 41 42 1.03 A 1 A A O CA VAL ALA 39 42 1.03 A 1 B B O CD1 GLN LEU 15 17 1.12 C 1 B B CA CD1 GLN LEU 15 17 1.31 C 1 B B CB CD2 GLN LEU 15 17 1.33 C 1 B B C C GLN LYS 15 16 1.35 B 1 B B O N GLN LEU 15 17 1.38 B 1 A A C C GLN LYS 15 16 1.41 B 1 A A CA N VAL ALA 39 42 1.44 A 1 A A O N GLN LEU 15 17 1.45 B 1 A A C CA GLN LEU 15 17 1.60 B 1 B B CB CG GLN LEU 15 17 1.64 C 1 A A N C VAL ALA 40 42 1.67 A 1 B B C CG GLN LEU 15 17 1.68 C 1 A A C CA VAL ALA 39 42 1.70 A 1 B B CG1 N ILE ALA 41 42 1.73 A 1 A A CB CB GLN LEU 15 17 1.83 B 1 B B CA CG GLN LEU 15 17 1.92 C 1 B B C CA GLN LEU 15 17 1.94 B 1 A A CB N VAL ALA 39 42 1.97 A 1 A A O CB VAL ALA 39 42 2.00 A 1 A A CA N GLN LEU 15 17 2.03 B 1 B B CB CD1 GLN LEU 15 17 2.08 C 1 B B CB CB GLN LEU 15 17 2.10 B 1 B B N CD1 GLN LEU 15 17 2.16 C 1 A A CA CA VAL ALA 39 42 2.16 A 1 A A C CB GLN LEU 15 17 2.17 B 1 A A C N VAL ALA 39 42 2.17 A 1 A A N CA VAL ALA 39 42 2.18 A 1 A A SER ASN 26 27 A A -149.52 1 A A C N GLN LYS 15 16 3.43 B 1 A A C N VAL ILE 40 41 4.68 B B 1 A A C N VAL ILE 40 41 7.99 A A 1 A A C N ILE ALA 41 42 5.78 A 1 B B C N GLN LYS 15 16 3.14 B 1 B B C N VAL ILE 40 41 2.90 B B 1 B B C N VAL ILE 40 41 7.66 A A 1 B B C N ILE ALA 41 42 3.60 A 1 -70.79 2.10 120.10 49.31 A A A CA C O ILE ILE ILE 41 41 41 A A N 1 -88.30 2.10 120.10 31.80 B B B CA C O ILE ILE ILE 41 41 41 A A N 1 A A C O ILE ILE 41 41 6.112 0.019 1.229 7.341 A N 1 B B C O ILE ILE 41 41 2.952 0.019 1.229 4.181 A N 1 A PHE 20 A -116.54 53.81 1 A LYS 28 B -156.59 89.34 1 A VAL 36 A 80.71 111.69 1 B LYS 28 B -174.89 117.87 1 B ALA 30 A -99.17 54.44 1 B VAL 36 A 67.08 116.96 5.00 1 5.00 0 388 0 0 388 AMYLOID BETA A4 PROTEIN Electron cryo-microscopy of an Abeta(1-42)amyloid fibril 1 N N 1 N N PROTEIN FIBRIL PROTEIN FIBRIL, ALZHEIMER'S DISEASE, AMYLOID FIBRIL, PROTEIN AGGREGATION, PROTEIN FOLDING, CROSS-BETA, FREALIX A GLY 37 A GLY 23 1 A GLY 38 A GLY 24 -25.15 B GLY 37 B GLY 23 1 B GLY 38 B GLY 24 -28.66 E9PG40_HUMAN UNP 1 E9PG40 630 657 5AEF 15 42 E9PG40 A 1 1 28 630 657 5AEF 15 42 E9PG40 B 1 1 28 2 2 2 2 4 2 2 4 4 parallel parallel parallel parallel parallel anti-parallel anti-parallel parallel parallel parallel parallel parallel parallel parallel parallel A LYS 16 A LYS 2 A VAL 18 A VAL 4 A LEU 17 A LEU 3 A PHE 19 A PHE 5 A GLY 33 A GLY 19 A LEU 34 A LEU 20 A ALA 30 A ALA 16 A GLY 37 A GLY 23 A ALA 30 A ALA 16 A ILE 32 A ILE 18 A ALA 30 A ALA 16 A GLY 37 A GLY 23 A MET 35 A MET 21 A VAL 40 A VAL 26 A ALA 30 A ALA 16 A GLY 37 A GLY 23 B LYS 16 B LYS 2 B PHE 19 B PHE 5 B LEU 17 B LEU 3 B PHE 20 B PHE 6 B PHE 19 B PHE 5 B PHE 20 B PHE 6 B LYS 16 B LYS 2 B PHE 19 B PHE 5 B ASN 27 B ASN 13 B LYS 28 B LYS 14 B ASN 27 B ASN 13 B LEU 34 B LEU 20 B ILE 32 B ILE 18 B GLY 33 B GLY 19 B ASN 27 B ASN 13 B LEU 34 B LEU 20 B MET 35 B MET 21 B VAL 36 B VAL 22 B LYS 28 B LYS 14 B VAL 36 B VAL 22 B ASN 27 B ASN 13 B LEU 34 B LEU 20 B ILE 32 B ILE 18 B GLY 33 B GLY 19 B MET 35 B MET 21 B VAL 36 B VAL 22 B LYS 28 B LYS 14 B VAL 36 B VAL 22 B ASN 27 B ASN 13 B LEU 34 B LEU 20 B ASN 27 B ASN 13 B LYS 28 B LYS 14 1 P 1