HEADER DE NOVO PROTEIN 03-DEC-24 9KU1 TITLE CRYO-ELECTRON MICROSCOPY STRUCTURE OF NANOFIBERS FORMED BY REVERSE TITLE 2 AZOBENZENE PEPTIDES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: AZOPEP; COMPND 3 CHAIN: A, B, C, D, E, F, G; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DE NOVO PROTEIN, NANOFIBER EXPDTA ELECTRON MICROSCOPY AUTHOR H.KAWABATA,H.UMEZAWA,S.Y.PARK REVDAT 1 10-JUN-26 9KU1 0 JRNL AUTH H.KAWABATA,H.UMEZAWA,S.Y.PARK JRNL TITL STRUCTURE OF AZOPEP PEPTIDE NANOFIBERS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 1.900 REMARK 3 NUMBER OF PARTICLES : 92358 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9KU1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300052506. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : AZOPEP PEPTIDE NANOFIBERS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEPTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 1 0.999549 -0.030015 0.000000 4.25253 REMARK 350 BIOMT2 1 0.030015 0.999549 0.000000 -4.12674 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -9.50640 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 3 -0.999747 0.022513 0.000000 275.99019 REMARK 350 BIOMT2 3 -0.022513 -0.999747 0.000000 282.27506 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -7.12980 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 4 0.999887 -0.015009 0.000000 2.11078 REMARK 350 BIOMT2 4 0.015009 0.999887 0.000000 -2.07933 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -4.75320 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 5 -0.999972 0.007505 0.000000 278.11651 REMARK 350 BIOMT2 5 -0.007505 -0.999972 0.000000 280.21163 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -2.37660 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 6 -0.999972 -0.007505 0.000000 280.21163 REMARK 350 BIOMT2 6 0.007505 -0.999972 0.000000 278.11651 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 2.37660 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 7 0.999887 0.015009 0.000000 -2.07933 REMARK 350 BIOMT2 7 -0.015009 0.999887 0.000000 2.11078 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 4.75320 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 103 O HOH C 107 2.11 REMARK 500 O HOH G 104 O HOH G 106 2.16 REMARK 500 O HOH C 108 O HOH D 103 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH G 109 DISTANCE = 7.71 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62572 RELATED DB: EMDB REMARK 900 STRUCTURE OF AZOPEP PEPTIDE NANOFIBERS DBREF 9KU1 A 0 8 PDB 9KU1 9KU1 0 8 DBREF 9KU1 B 0 8 PDB 9KU1 9KU1 0 8 DBREF 9KU1 C 0 8 PDB 9KU1 9KU1 0 8 DBREF 9KU1 D 0 8 PDB 9KU1 9KU1 0 8 DBREF 9KU1 E 0 8 PDB 9KU1 9KU1 0 8 DBREF 9KU1 F 0 8 PDB 9KU1 9KU1 0 8 DBREF 9KU1 G 0 8 PDB 9KU1 9KU1 0 8 SEQRES 1 A 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 SEQRES 1 B 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 SEQRES 1 C 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 SEQRES 1 D 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 SEQRES 1 E 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 SEQRES 1 F 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 SEQRES 1 G 9 ACE ARG MET ASP ALA ARG OZW ARG NH2 HET ACE A 0 3 HET OZW A 6 19 HET NH2 A 8 1 HET ACE B 0 3 HET OZW B 6 19 HET NH2 B 8 1 HET ACE C 0 3 HET OZW C 6 19 HET NH2 C 8 1 HET ACE D 0 3 HET OZW D 6 19 HET NH2 D 8 1 HET ACE E 0 3 HET OZW E 6 19 HET NH2 E 8 1 HET ACE F 0 3 HET OZW F 6 19 HET NH2 F 8 1 HET ACE G 0 3 HET OZW G 6 19 HET NH2 G 8 1 HETNAM ACE ACETYL GROUP HETNAM OZW PHENYLHYDRAZINYL PHENYLALANINE HETNAM NH2 AMINO GROUP FORMUL 1 ACE 7(C2 H4 O) FORMUL 1 OZW 7(C15 H17 N3 O2) FORMUL 1 NH2 7(H2 N) FORMUL 8 HOH *36(H2 O) LINK C ACE A 0 N ARG A 1 1555 1555 1.34 LINK C ARG A 5 N OZW A 6 1555 1555 1.34 LINK C OZW A 6 N ARG A 7 1555 1555 1.33 LINK C ARG A 7 N NH2 A 8 1555 1555 1.34 LINK C ACE B 0 N ARG B 1 1555 1555 1.33 LINK C ARG B 5 N OZW B 6 1555 1555 1.33 LINK C OZW B 6 N ARG B 7 1555 1555 1.33 LINK C ARG B 7 N NH2 B 8 1555 1555 1.34 LINK C ACE C 0 N ARG C 1 1555 1555 1.34 LINK C ARG C 5 N OZW C 6 1555 1555 1.33 LINK C OZW C 6 N ARG C 7 1555 1555 1.33 LINK C ARG C 7 N NH2 C 8 1555 1555 1.33 LINK C ACE D 0 N ARG D 1 1555 1555 1.34 LINK C ARG D 5 N OZW D 6 1555 1555 1.34 LINK C OZW D 6 N ARG D 7 1555 1555 1.33 LINK C ARG D 7 N NH2 D 8 1555 1555 1.34 LINK C ACE E 0 N ARG E 1 1555 1555 1.34 LINK C ARG E 5 N OZW E 6 1555 1555 1.34 LINK C OZW E 6 N ARG E 7 1555 1555 1.34 LINK C ARG E 7 N NH2 E 8 1555 1555 1.34 LINK C ACE F 0 N ARG F 1 1555 1555 1.33 LINK C ARG F 5 N OZW F 6 1555 1555 1.33 LINK C OZW F 6 N ARG F 7 1555 1555 1.33 LINK C ARG F 7 N NH2 F 8 1555 1555 1.34 LINK C ACE G 0 N ARG G 1 1555 1555 1.34 LINK C ARG G 5 N OZW G 6 1555 1555 1.33 LINK C OZW G 6 N ARG G 7 1555 1555 1.33 LINK C ARG G 7 N NH2 G 8 1555 1555 1.35 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MTRIX1 54 0.999549 -0.030015 0.000000 4.25253 MTRIX2 54 0.030015 0.999549 0.000000 -4.12674 MTRIX3 54 0.000000 0.000000 1.000000 -9.50640 MTRIX1 55 -0.999747 0.022513 0.000000 275.99019 MTRIX2 55 -0.022513 -0.999747 0.000000 282.27506 MTRIX3 55 0.000000 0.000000 1.000000 -7.12980 MTRIX1 56 0.999887 -0.015009 0.000000 2.11078 MTRIX2 56 0.015009 0.999887 0.000000 -2.07933 MTRIX3 56 0.000000 0.000000 1.000000 -4.75320 MTRIX1 57 -0.999972 0.007505 0.000000 278.11651 MTRIX2 57 -0.007505 -0.999972 0.000000 280.21163 MTRIX3 57 0.000000 0.000000 1.000000 -2.37660 MTRIX1 59 -0.999972 -0.007505 0.000000 280.21163 MTRIX2 59 0.007505 -0.999972 0.000000 278.11651 MTRIX3 59 0.000000 0.000000 1.000000 2.37660 MTRIX1 60 0.999887 0.015009 0.000000 -2.07933 MTRIX2 60 -0.015009 0.999887 0.000000 2.11078 MTRIX3 60 0.000000 0.000000 1.000000 4.75320 MTRIX1 62 0.999549 0.030015 0.000000 -4.12674 MTRIX2 62 -0.030015 0.999549 0.000000 4.25253 MTRIX3 62 0.000000 0.000000 1.000000 9.50640 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 38 53 CONECT 47 48 51 CONECT 48 47 52 CONECT 49 50 51 64 CONECT 50 49 52 CONECT 51 47 49 CONECT 52 48 50 CONECT 53 38 54 CONECT 54 53 55 57 CONECT 55 54 56 66 CONECT 56 55 CONECT 57 54 58 CONECT 58 57 59 60 CONECT 59 58 61 CONECT 60 58 62 CONECT 61 59 63 CONECT 62 60 63 CONECT 63 61 62 65 CONECT 64 49 65 CONECT 65 63 64 CONECT 66 55 CONECT 68 77 CONECT 77 68 CONECT 79 80 81 82 CONECT 80 79 CONECT 81 79 CONECT 82 79 CONECT 116 131 CONECT 125 126 129 CONECT 126 125 130 CONECT 127 128 129 142 CONECT 128 127 130 CONECT 129 125 127 CONECT 130 126 128 CONECT 131 116 132 CONECT 132 131 133 135 CONECT 133 132 134 144 CONECT 134 133 CONECT 135 132 136 CONECT 136 135 137 138 CONECT 137 136 139 CONECT 138 136 140 CONECT 139 137 141 CONECT 140 138 141 CONECT 141 139 140 143 CONECT 142 127 143 CONECT 143 141 142 CONECT 144 133 CONECT 146 155 CONECT 155 146 CONECT 157 158 159 160 CONECT 158 157 CONECT 159 157 CONECT 160 157 CONECT 194 209 CONECT 203 204 207 CONECT 204 203 208 CONECT 205 206 207 220 CONECT 206 205 208 CONECT 207 203 205 CONECT 208 204 206 CONECT 209 194 210 CONECT 210 209 211 213 CONECT 211 210 212 222 CONECT 212 211 CONECT 213 210 214 CONECT 214 213 215 216 CONECT 215 214 217 CONECT 216 214 218 CONECT 217 215 219 CONECT 218 216 219 CONECT 219 217 218 221 CONECT 220 205 221 CONECT 221 219 220 CONECT 222 211 CONECT 224 233 CONECT 233 224 CONECT 235 236 237 238 CONECT 236 235 CONECT 237 235 CONECT 238 235 CONECT 272 287 CONECT 281 282 285 CONECT 282 281 286 CONECT 283 284 285 298 CONECT 284 283 286 CONECT 285 281 283 CONECT 286 282 284 CONECT 287 272 288 CONECT 288 287 289 291 CONECT 289 288 290 300 CONECT 290 289 CONECT 291 288 292 CONECT 292 291 293 294 CONECT 293 292 295 CONECT 294 292 296 CONECT 295 293 297 CONECT 296 294 297 CONECT 297 295 296 299 CONECT 298 283 299 CONECT 299 297 298 CONECT 300 289 CONECT 302 311 CONECT 311 302 CONECT 313 314 315 316 CONECT 314 313 CONECT 315 313 CONECT 316 313 CONECT 350 365 CONECT 359 360 363 CONECT 360 359 364 CONECT 361 362 363 376 CONECT 362 361 364 CONECT 363 359 361 CONECT 364 360 362 CONECT 365 350 366 CONECT 366 365 367 369 CONECT 367 366 368 378 CONECT 368 367 CONECT 369 366 370 CONECT 370 369 371 372 CONECT 371 370 373 CONECT 372 370 374 CONECT 373 371 375 CONECT 374 372 375 CONECT 375 373 374 377 CONECT 376 361 377 CONECT 377 375 376 CONECT 378 367 CONECT 380 389 CONECT 389 380 CONECT 391 392 393 394 CONECT 392 391 CONECT 393 391 CONECT 394 391 CONECT 428 443 CONECT 437 438 441 CONECT 438 437 442 CONECT 439 440 441 454 CONECT 440 439 442 CONECT 441 437 439 CONECT 442 438 440 CONECT 443 428 444 CONECT 444 443 445 447 CONECT 445 444 446 456 CONECT 446 445 CONECT 447 444 448 CONECT 448 447 449 450 CONECT 449 448 451 CONECT 450 448 452 CONECT 451 449 453 CONECT 452 450 453 CONECT 453 451 452 455 CONECT 454 439 455 CONECT 455 453 454 CONECT 456 445 CONECT 458 467 CONECT 467 458 CONECT 469 470 471 472 CONECT 470 469 CONECT 471 469 CONECT 472 469 CONECT 506 521 CONECT 515 516 519 CONECT 516 515 520 CONECT 517 518 519 532 CONECT 518 517 520 CONECT 519 515 517 CONECT 520 516 518 CONECT 521 506 522 CONECT 522 521 523 525 CONECT 523 522 524 534 CONECT 524 523 CONECT 525 522 526 CONECT 526 525 527 528 CONECT 527 526 529 CONECT 528 526 530 CONECT 529 527 531 CONECT 530 528 531 CONECT 531 529 530 533 CONECT 532 517 533 CONECT 533 531 532 CONECT 534 523 CONECT 536 545 CONECT 545 536 MASTER 146 0 21 0 0 0 0 27 575 7 189 7 END