1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0001-7495-4219 Kawabata, H. 0009-0003-5055-0297 Umezawa, H. 0000-0001-6164-8896 Park, S.Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 90.00 90.00 90.00 1.00 1.00 1.00 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking H2 O 18.015 WATER non-polymer C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking H2 N 16.023 AMINO GROUP non-polymer C15 H17 N3 O2 271.314 n phenylhydrazinyl phenylalanine L-peptide linking N 1 N C N 2 N O N 3 N C N 4 N H N 5 N H N 6 N H N 7 N H N 8 N N N 9 S C N 10 N C N 11 N O N 12 N C N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N N N 22 S C N 23 N C N 24 N O N 25 N C N 26 N C N 27 N C N 28 N N N 29 N C N 30 N N N 31 N N N 32 N O N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H 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 N N 49 S C N 50 N C N 51 N O N 52 N C N 53 N C N 54 N O N 55 N O N 56 N O N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N O N 65 N H N 66 N H N 67 N N N 68 S C N 69 N C N 70 N O N 71 N C N 72 N C N 73 N S N 74 N C N 75 N O N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N N N 88 N H N 89 N H Y 90 N C Y 91 N C Y 92 N C Y 93 N C Y 94 N C Y 95 N C N 96 N N N 97 S C N 98 N C N 99 N O N 100 N C Y 101 N C Y 102 N C Y 103 N C Y 104 N C Y 105 N C Y 106 N C N 107 N N N 108 N N N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N O N 126 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub 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 sing N 24 N sing N 25 N doub N 26 N sing N 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 sing N 38 N sing N 39 N doub 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 doub N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N doub 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 doub 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 sing N 80 N sing N 81 N sing N 82 N sing N 83 N doub N 84 N sing Y 85 N doub Y 86 N sing N 87 N sing N 88 N sing N 89 N sing Y 90 N sing Y 91 N doub N 92 N sing Y 93 N doub Y 94 N sing N 95 N sing Y 96 N doub Y 97 N sing N 98 N sing Y 99 N sing Y 100 N doub Y 101 N doub Y 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing To Be Published 0353 Structure of AzoPep peptide nanofibers 0000-0001-7495-4219 0009-0003-5055-0297 0000-0001-6164-8896 10.2210/pdb9ku1/pdb pdb_00009ku1 9KU1 92358 1.9 FSC 0.143 CUT-OFF HELICAL REL 2024-12-03 PDBJ 2026-06-10 2026-06-10 Cryo-electron microscopy structure of nanofibers formed by reverse azobenzene peptides. 7 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 AzoPep peptide nanofibers 0 SYNTHETIC COMPLEX 32630 synthetic construct FILAMENT 1 1 HELICAL 179.57 2.3766 C1 50 FEI FALCON IV (4k x 4k) 300 FIELD EMISSION GUN FLOOD BEAM TFS KRIOS BRIGHT FIELD 2000 800 1 PARTICLE SELECTION 1 IMAGE ACQUISITION 1 MASKING CTF CORRECTION 1 LAYERLINE INDEXING DIFFRACTION INDEXING MODEL FITTING MODEL REFINEMENT OTHER INITIAL EULER ASSIGNMENT 1 FINAL EULER ASSIGNMENT 1 CLASSIFICATION 1 RECONSTRUCTION 1 NO NO NO YES ETHANE 9KU1 1084.302 AzoPep 7 syn polymer 18.015 water 36 nat water no yes (ACE)RMDAR(OZW)R(NH2) XRMDARFRX A,B,C,D,E,F,G polypeptide(L) n n n n n n n n n repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release repository Initial release 1 0 2026-06-10 1 0 2026-06-10 1 0 1 2026-06-10 1 0 2026-06-10 1 0 1 2026-06-10 1 0 2 2026-06-10 1 0 2026-06-10 1 0 1 2026-06-10 1 0 2026-06-10 Not funded park@yokohama-cu.ac.jp 0000-0001-6164-8896 Sam-Yong Park principal investigator/group leader Structure of AzoPep peptide nanofibers N PDBJ Y PDBJ 2024-12-03 REL 1 G O HOH 109 7.71 ACE ACE SUBJECT OF INVESTIGATION OZW OZW SUBJECT OF INVESTIGATION NH2 NH2 SUBJECT OF INVESTIGATION HOH water 32630 synthetic construct sample 1 9 Y Y A OZW 6 Non-standard residue A OZW 7 OZW 1 1_555 None B OZW 6 Non-standard residue B OZW 7 OZW 1 1_555 None C OZW 6 Non-standard residue C OZW 7 OZW 1 1_555 None D OZW 6 Non-standard residue D OZW 7 OZW 1 1_555 None E OZW 6 Non-standard residue E OZW 7 OZW 1 1_555 None F OZW 6 Non-standard residue F OZW 7 OZW 1 1_555 None G OZW 6 Non-standard residue G OZW 7 OZW 1 1_555 None A ACE 0 Terminal acetylation A ACE 1 A ARG 1 ARG A ARG 2 1_555 ACE 8 1_555 None B ACE 0 Terminal acetylation B ACE 1 B ARG 1 ARG B ARG 2 1_555 ACE 8 1_555 None C ACE 0 Terminal acetylation C ACE 1 C ARG 1 ARG C ARG 2 1_555 ACE 8 1_555 None D ACE 0 Terminal acetylation D ACE 1 D ARG 1 ARG D ARG 2 1_555 ACE 8 1_555 None E ACE 0 Terminal acetylation E ACE 1 E ARG 1 ARG E ARG 2 1_555 ACE 8 1_555 None F ACE 0 Terminal acetylation F ACE 1 F ARG 1 ARG F ARG 2 1_555 ACE 8 1_555 None G ACE 0 Terminal acetylation G ACE 1 G ARG 1 ARG G ARG 2 1_555 ACE 8 1_555 None A NH2 8 Terminal amidation A NH2 9 A ARG 7 ARG A ARG 8 1_555 NH2 8 1_555 None B NH2 8 Terminal amidation B NH2 9 B ARG 7 ARG B ARG 8 1_555 NH2 8 1_555 None C NH2 8 Terminal amidation C NH2 9 C ARG 7 ARG C ARG 8 1_555 NH2 8 1_555 None D NH2 8 Terminal amidation D NH2 9 D ARG 7 ARG D ARG 8 1_555 NH2 8 1_555 None E NH2 8 Terminal amidation E NH2 9 E ARG 7 ARG E ARG 8 1_555 NH2 8 1_555 None F NH2 8 Terminal amidation F NH2 9 F ARG 7 ARG F ARG 8 1_555 NH2 8 1_555 None G NH2 8 Terminal amidation G NH2 9 G ARG 7 ARG G ARG 8 1_555 NH2 8 1_555 None HOH 30 2 HOH HOH 101 A HOH 12 2 HOH HOH 102 A HOH 1 2 HOH HOH 103 A HOH 32 2 HOH HOH 104 A HOH 20 2 HOH HOH 101 B HOH 2 2 HOH HOH 102 B HOH 21 2 HOH HOH 101 C HOH 13 2 HOH HOH 102 C HOH 19 2 HOH HOH 103 C HOH 14 2 HOH HOH 104 C HOH 3 2 HOH HOH 105 C HOH 11 2 HOH HOH 106 C HOH 7 2 HOH HOH 107 C HOH 4 2 HOH HOH 108 C HOH 15 2 HOH HOH 101 D HOH 35 2 HOH HOH 102 D HOH 16 2 HOH HOH 103 D HOH 18 2 HOH HOH 104 D HOH 17 2 HOH HOH 105 D HOH 6 2 HOH HOH 106 D HOH 23 2 HOH HOH 101 E HOH 22 2 HOH HOH 102 E HOH 8 2 HOH HOH 103 E HOH 25 2 HOH HOH 101 F HOH 24 2 HOH HOH 102 F HOH 9 2 HOH HOH 103 F HOH 26 2 HOH HOH 104 F HOH 5 2 HOH HOH 101 G HOH 31 2 HOH HOH 102 G HOH 28 2 HOH HOH 103 G HOH 29 2 HOH HOH 104 G HOH 27 2 HOH HOH 105 G HOH 10 2 HOH HOH 106 G HOH 33 2 HOH HOH 107 G HOH 36 2 HOH HOH 108 G HOH 34 2 HOH HOH 109 G ACE 0 n 1 ACE 0 A ARG 1 n 2 ARG 1 A MET 2 n 3 MET 2 A ASP 3 n 4 ASP 3 A ALA 4 n 5 ALA 4 A ARG 5 n 6 ARG 5 A AZP 6 n 7 OZW 6 A ARG 7 n 8 ARG 7 A NH2 8 n 9 NH2 8 A ACE 0 n 1 ACE 0 B ARG 1 n 2 ARG 1 B MET 2 n 3 MET 2 B ASP 3 n 4 ASP 3 B ALA 4 n 5 ALA 4 B ARG 5 n 6 ARG 5 B AZP 6 n 7 OZW 6 B ARG 7 n 8 ARG 7 B NH2 8 n 9 NH2 8 B ACE 0 n 1 ACE 0 C ARG 1 n 2 ARG 1 C MET 2 n 3 MET 2 C ASP 3 n 4 ASP 3 C ALA 4 n 5 ALA 4 C ARG 5 n 6 ARG 5 C AZP 6 n 7 OZW 6 C ARG 7 n 8 ARG 7 C NH2 8 n 9 NH2 8 C ACE 0 n 1 ACE 0 D ARG 1 n 2 ARG 1 D MET 2 n 3 MET 2 D ASP 3 n 4 ASP 3 D ALA 4 n 5 ALA 4 D ARG 5 n 6 ARG 5 D AZP 6 n 7 OZW 6 D ARG 7 n 8 ARG 7 D NH2 8 n 9 NH2 8 D ACE 0 n 1 ACE 0 E ARG 1 n 2 ARG 1 E MET 2 n 3 MET 2 E ASP 3 n 4 ASP 3 E ALA 4 n 5 ALA 4 E ARG 5 n 6 ARG 5 E AZP 6 n 7 OZW 6 E ARG 7 n 8 ARG 7 E NH2 8 n 9 NH2 8 E ACE 0 n 1 ACE 0 F ARG 1 n 2 ARG 1 F MET 2 n 3 MET 2 F ASP 3 n 4 ASP 3 F ALA 4 n 5 ALA 4 F ARG 5 n 6 ARG 5 F AZP 6 n 7 OZW 6 F ARG 7 n 8 ARG 7 F NH2 8 n 9 NH2 8 F ACE 0 n 1 ACE 0 G ARG 1 n 2 ARG 1 G MET 2 n 3 MET 2 G ASP 3 n 4 ASP 3 G ALA 4 n 5 ALA 4 G ARG 5 n 6 ARG 5 G AZP 6 n 7 OZW 6 G ARG 7 n 8 ARG 7 G NH2 8 n 9 NH2 8 G author_defined_assembly 7 heptameric not applicable electron microscopy 0.999549 -0.030015 0.000000 0.030015 0.999549 0.000000 0.000000 0.000000 1.000000 point symmetry operation 4.25253 -4.12674 -9.50640 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 1_555 x,y,z identity operation 0.0 0.0 0.0 -0.999747 0.022513 0.000000 -0.022513 -0.999747 0.000000 0.000000 0.000000 1.000000 point symmetry operation 275.99019 282.27506 -7.12980 0.999887 -0.015009 0.000000 0.015009 0.999887 0.000000 0.000000 0.000000 1.000000 point symmetry operation 2.11078 -2.07933 -4.75320 -0.999972 0.007505 0.000000 -0.007505 -0.999972 0.000000 0.000000 0.000000 1.000000 point symmetry operation 278.11651 280.21163 -2.37660 -0.999972 -0.007505 0.000000 0.007505 -0.999972 0.000000 0.000000 0.000000 1.000000 point symmetry operation 280.21163 278.11651 2.37660 0.999887 0.015009 0.000000 -0.015009 0.999887 0.000000 0.000000 0.000000 1.000000 point symmetry operation -2.07933 2.11078 4.75320 1 C C O O HOH HOH 103 107 2.11 1 G G O O HOH HOH 104 106 2.16 1 C D O O HOH HOH 108 103 2.18 N Cryo-electron microscopy structure of nanofibers formed by reverse azobenzene peptides. 1 N N 1 N N 1 N N 1 N N 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N covale 1.337 both A ACE 0 A C ACE 1 1_555 A ARG 1 A N ARG 2 1_555 covale 1.341 both A ARG 5 A C ARG 6 1_555 A OZW 6 A N OZW 7 1_555 covale 1.332 both A OZW 6 A C OZW 7 1_555 A ARG 7 A N ARG 8 1_555 covale 1.335 both A ARG 7 A C ARG 8 1_555 A NH2 8 A N NH2 9 1_555 covale 1.334 both B ACE 0 B C ACE 1 1_555 B ARG 1 B N ARG 2 1_555 covale 1.333 both B ARG 5 B C ARG 6 1_555 B OZW 6 B N OZW 7 1_555 covale 1.330 both B OZW 6 B C OZW 7 1_555 B ARG 7 B N ARG 8 1_555 covale 1.338 both B ARG 7 B C ARG 8 1_555 B NH2 8 B N NH2 9 1_555 covale 1.338 both C ACE 0 C C ACE 1 1_555 C ARG 1 C N ARG 2 1_555 covale 1.331 both C ARG 5 C C ARG 6 1_555 C OZW 6 C N OZW 7 1_555 covale 1.328 both C OZW 6 C C OZW 7 1_555 C ARG 7 C N ARG 8 1_555 covale 1.329 both C ARG 7 C C ARG 8 1_555 C NH2 8 C N NH2 9 1_555 covale 1.337 both D ACE 0 D C ACE 1 1_555 D ARG 1 D N ARG 2 1_555 covale 1.335 both D ARG 5 D C ARG 6 1_555 D OZW 6 D N OZW 7 1_555 covale 1.330 both D OZW 6 D C OZW 7 1_555 D ARG 7 D N ARG 8 1_555 covale 1.335 both D ARG 7 D C ARG 8 1_555 D NH2 8 D N NH2 9 1_555 covale 1.338 both E ACE 0 E C ACE 1 1_555 E ARG 1 E N ARG 2 1_555 covale 1.335 both E ARG 5 E C ARG 6 1_555 E OZW 6 E N OZW 7 1_555 covale 1.336 both E OZW 6 E C OZW 7 1_555 E ARG 7 E N ARG 8 1_555 covale 1.340 both E ARG 7 E C ARG 8 1_555 E NH2 8 E N NH2 9 1_555 covale 1.334 both F ACE 0 F C ACE 1 1_555 F ARG 1 F N ARG 2 1_555 covale 1.333 both F ARG 5 F C ARG 6 1_555 F OZW 6 F N OZW 7 1_555 covale 1.327 both F OZW 6 F C OZW 7 1_555 F ARG 7 F N ARG 8 1_555 covale 1.338 both F ARG 7 F C ARG 8 1_555 F NH2 8 F N NH2 9 1_555 covale 1.337 both G ACE 0 G C ACE 1 1_555 G ARG 1 G N ARG 2 1_555 covale 1.330 both G ARG 5 G C ARG 6 1_555 G OZW 6 G N OZW 7 1_555 covale 1.332 both G OZW 6 G C OZW 7 1_555 G ARG 7 G N ARG 8 1_555 covale 1.348 both G ARG 7 G C ARG 8 1_555 G NH2 8 G N NH2 9 1_555 DE NOVO PROTEIN de novo protein, nanofiber generate 0.999549 -0.030015 0.000000 0.030015 0.999549 0.000000 0.000000 0.000000 1.000000 4.25253 -4.12674 -9.50640 generate -0.999747 0.022513 0.000000 -0.022513 -0.999747 0.000000 0.000000 0.000000 1.000000 275.99019 282.27506 -7.12980 generate 0.999887 -0.015009 0.000000 0.015009 0.999887 0.000000 0.000000 0.000000 1.000000 2.11078 -2.07933 -4.75320 generate -0.999972 0.007505 0.000000 -0.007505 -0.999972 0.000000 0.000000 0.000000 1.000000 278.11651 280.21163 -2.37660 generate -0.999972 -0.007505 0.000000 0.007505 -0.999972 0.000000 0.000000 0.000000 1.000000 280.21163 278.11651 2.37660 generate 0.999887 0.015009 0.000000 -0.015009 0.999887 0.000000 0.000000 0.000000 1.000000 -2.07933 2.11078 4.75320 generate 0.999549 0.030015 0.000000 -0.030015 0.999549 0.000000 0.000000 0.000000 1.000000 -4.12674 4.25253 9.50640 9KU1 PDB 1 1 9KU1 0 8 9KU1 0 8 9KU1 A 1 1 9 0 8 9KU1 0 8 9KU1 B 1 1 9 0 8 9KU1 0 8 9KU1 C 1 1 9 0 8 9KU1 0 8 9KU1 D 1 1 9 0 8 9KU1 0 8 9KU1 E 1 1 9 0 8 9KU1 0 8 9KU1 F 1 1 9 0 8 9KU1 0 8 9KU1 G 1 1 9 1 P 1