HEADER DE NOVO PROTEIN 30-JUL-25 9W3T TITLE CRYO-ELECTRON MICROSCOPY STRUCTURE OF NANOFIBERS FORMED BY AZOBENZENE TITLE 2 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 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS DE NOVO PROTEIN, NANOFIBER EXPDTA ELECTRON MICROSCOPY AUTHOR H.KAWABATA,S.Y.PARK REVDAT 1 05-AUG-26 9W3T 0 JRNL AUTH H.KAWABATA,S.Y.PARK JRNL TITL STRUCTURE OF AZOPEP PEPTIDE NANOFIBERS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, RELION 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) : 2.330 REMARK 3 NUMBER OF PARTICLES : 106867 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 9W3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300061870. 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: 98-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 98-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 1 0.998103 -0.061567 0.000000 5.90572 REMARK 350 BIOMT2 1 0.061567 0.998103 0.000000 -5.55266 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -14.22213 REMARK 350 BIOMT1 2 -0.998103 0.061567 0.000000 180.20628 REMARK 350 BIOMT2 2 -0.061567 -0.998103 0.000000 191.66466 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -14.22213 REMARK 350 BIOMT1 3 0.999157 -0.041059 0.000000 3.89928 REMARK 350 BIOMT2 3 0.041059 0.999157 0.000000 -3.74233 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -9.48142 REMARK 350 BIOMT1 4 -0.999157 0.041059 0.000000 182.21272 REMARK 350 BIOMT2 4 -0.041059 -0.999157 0.000000 189.85433 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -9.48142 REMARK 350 BIOMT1 5 0.999789 -0.020534 0.000000 1.93043 REMARK 350 BIOMT2 5 0.020534 0.999789 0.000000 -1.89118 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -4.74071 REMARK 350 BIOMT1 6 -0.999789 0.020534 0.000000 184.18157 REMARK 350 BIOMT2 6 -0.020534 -0.999789 0.000000 188.00318 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -4.74071 REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 186.11200 REMARK 350 BIOMT2 8 0.000000 -1.000000 0.000000 186.11200 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 0.999789 0.020534 0.000000 -1.89118 REMARK 350 BIOMT2 9 -0.020534 0.999789 0.000000 1.93043 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 4.74071 REMARK 350 BIOMT1 10 -0.999789 -0.020534 0.000000 188.00318 REMARK 350 BIOMT2 10 0.020534 -0.999789 0.000000 184.18157 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 4.74071 REMARK 350 BIOMT1 11 0.999157 0.041059 0.000000 -3.74233 REMARK 350 BIOMT2 11 -0.041059 0.999157 0.000000 3.89928 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 9.48142 REMARK 350 BIOMT1 12 -0.999157 -0.041059 0.000000 189.85433 REMARK 350 BIOMT2 12 0.041059 -0.999157 0.000000 182.21272 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 9.48142 REMARK 350 BIOMT1 13 0.998103 0.061567 0.000000 -5.55266 REMARK 350 BIOMT2 13 -0.061567 0.998103 0.000000 5.90572 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 14.22213 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-65607 RELATED DB: EMDB REMARK 900 CRYO-ELECTRON MICROSCOPY STRUCTURE OF NANOFIBERS FORMED BY REMARK 900 AZOBENZENE PEPTIDES. DBREF 9W3T A 0 8 PDB 9W3T 9W3T 0 8 DBREF 9W3T B 0 8 PDB 9W3T 9W3T 0 8 DBREF 9W3T C 0 8 PDB 9W3T 9W3T 0 8 DBREF 9W3T D 0 8 PDB 9W3T 9W3T 0 8 DBREF 9W3T E 0 8 PDB 9W3T 9W3T 0 8 DBREF 9W3T F 0 8 PDB 9W3T 9W3T 0 8 DBREF 9W3T G 0 8 PDB 9W3T 9W3T 0 8 SEQRES 1 A 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 SEQRES 1 B 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 SEQRES 1 C 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 SEQRES 1 D 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 SEQRES 1 E 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 SEQRES 1 F 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 SEQRES 1 G 9 ACE ARG OZW ARG ALA ASP MET ARG NH2 HET ACE A 0 3 HET OZW A 2 19 HET NH2 A 8 1 HET ACE B 0 3 HET OZW B 2 19 HET NH2 B 8 1 HET ACE C 0 3 HET OZW C 2 19 HET NH2 C 8 1 HET ACE D 0 3 HET OZW D 2 19 HET NH2 D 8 1 HET ACE E 0 3 HET OZW E 2 19 HET NH2 E 8 1 HET ACE F 0 3 HET OZW F 2 19 HET NH2 F 8 1 HET ACE G 0 3 HET OZW G 2 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 *18(H2 O) LINK C ACE A 0 N ARG A 1 1555 1555 1.37 LINK C ARG A 1 N OZW A 2 1555 1555 1.34 LINK C OZW A 2 N ARG A 3 1555 1555 1.35 LINK C ARG A 7 N NH2 A 8 1555 1555 1.32 LINK C ACE B 0 N ARG B 1 1555 1555 1.35 LINK C ARG B 1 N OZW B 2 1555 1555 1.34 LINK C OZW B 2 N ARG B 3 1555 1555 1.34 LINK C ARG B 7 N NH2 B 8 1555 1555 1.33 LINK C ACE C 0 N ARG C 1 1555 1555 1.33 LINK C ARG C 1 N OZW C 2 1555 1555 1.35 LINK C OZW C 2 N ARG C 3 1555 1555 1.33 LINK C ARG C 7 N NH2 C 8 1555 1555 1.34 LINK C ACE D 0 N ARG D 1 1555 1555 1.34 LINK C ARG D 1 N OZW D 2 1555 1555 1.36 LINK C OZW D 2 N ARG D 3 1555 1555 1.35 LINK C ARG D 7 N NH2 D 8 1555 1555 1.33 LINK C ACE E 0 N ARG E 1 1555 1555 1.28 LINK C ARG E 1 N OZW E 2 1555 1555 1.31 LINK C OZW E 2 N ARG E 3 1555 1555 1.33 LINK C ARG E 7 N NH2 E 8 1555 1555 1.33 LINK C ACE F 0 N ARG F 1 1555 1555 1.37 LINK C ARG F 1 N OZW F 2 1555 1555 1.34 LINK C OZW F 2 N ARG F 3 1555 1555 1.34 LINK C ARG F 7 N NH2 F 8 1555 1555 1.32 LINK C ACE G 0 N ARG G 1 1555 1555 1.29 LINK C ARG G 1 N OZW G 2 1555 1555 1.30 LINK C OZW G 2 N ARG G 3 1555 1555 1.33 LINK C ARG G 7 N NH2 G 8 1555 1555 1.33 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 CONECT 1 2 3 4 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 6 21 CONECT 15 16 19 CONECT 16 15 20 CONECT 17 18 19 32 CONECT 18 17 20 CONECT 19 15 17 CONECT 20 16 18 CONECT 21 6 22 CONECT 22 21 23 25 CONECT 23 22 24 34 CONECT 24 23 CONECT 25 22 26 CONECT 26 25 27 28 CONECT 27 26 29 CONECT 28 26 30 CONECT 29 27 31 CONECT 30 28 31 CONECT 31 29 30 33 CONECT 32 17 33 CONECT 33 31 32 CONECT 34 23 CONECT 68 77 CONECT 77 68 CONECT 79 80 81 82 CONECT 80 79 CONECT 81 79 CONECT 82 79 CONECT 84 99 CONECT 93 94 97 CONECT 94 93 98 CONECT 95 96 97 110 CONECT 96 95 98 CONECT 97 93 95 CONECT 98 94 96 CONECT 99 84 100 CONECT 100 99 101 103 CONECT 101 100 102 112 CONECT 102 101 CONECT 103 100 104 CONECT 104 103 105 106 CONECT 105 104 107 CONECT 106 104 108 CONECT 107 105 109 CONECT 108 106 109 CONECT 109 107 108 111 CONECT 110 95 111 CONECT 111 109 110 CONECT 112 101 CONECT 146 155 CONECT 155 146 CONECT 157 158 159 160 CONECT 158 157 CONECT 159 157 CONECT 160 157 CONECT 162 177 CONECT 171 172 175 CONECT 172 171 176 CONECT 173 174 175 188 CONECT 174 173 176 CONECT 175 171 173 CONECT 176 172 174 CONECT 177 162 178 CONECT 178 177 179 181 CONECT 179 178 180 190 CONECT 180 179 CONECT 181 178 182 CONECT 182 181 183 184 CONECT 183 182 185 CONECT 184 182 186 CONECT 185 183 187 CONECT 186 184 187 CONECT 187 185 186 189 CONECT 188 173 189 CONECT 189 187 188 CONECT 190 179 CONECT 224 233 CONECT 233 224 CONECT 235 236 237 238 CONECT 236 235 CONECT 237 235 CONECT 238 235 CONECT 240 255 CONECT 249 250 253 CONECT 250 249 254 CONECT 251 252 253 266 CONECT 252 251 254 CONECT 253 249 251 CONECT 254 250 252 CONECT 255 240 256 CONECT 256 255 257 259 CONECT 257 256 258 268 CONECT 258 257 CONECT 259 256 260 CONECT 260 259 261 262 CONECT 261 260 263 CONECT 262 260 264 CONECT 263 261 265 CONECT 264 262 265 CONECT 265 263 264 267 CONECT 266 251 267 CONECT 267 265 266 CONECT 268 257 CONECT 302 311 CONECT 311 302 CONECT 313 314 315 316 CONECT 314 313 CONECT 315 313 CONECT 316 313 CONECT 318 333 CONECT 327 328 331 CONECT 328 327 332 CONECT 329 330 331 344 CONECT 330 329 332 CONECT 331 327 329 CONECT 332 328 330 CONECT 333 318 334 CONECT 334 333 335 337 CONECT 335 334 336 346 CONECT 336 335 CONECT 337 334 338 CONECT 338 337 339 340 CONECT 339 338 341 CONECT 340 338 342 CONECT 341 339 343 CONECT 342 340 343 CONECT 343 341 342 345 CONECT 344 329 345 CONECT 345 343 344 CONECT 346 335 CONECT 380 389 CONECT 389 380 CONECT 391 392 393 394 CONECT 392 391 CONECT 393 391 CONECT 394 391 CONECT 396 411 CONECT 405 406 409 CONECT 406 405 410 CONECT 407 408 409 422 CONECT 408 407 410 CONECT 409 405 407 CONECT 410 406 408 CONECT 411 396 412 CONECT 412 411 413 415 CONECT 413 412 414 424 CONECT 414 413 CONECT 415 412 416 CONECT 416 415 417 418 CONECT 417 416 419 CONECT 418 416 420 CONECT 419 417 421 CONECT 420 418 421 CONECT 421 419 420 423 CONECT 422 407 423 CONECT 423 421 422 CONECT 424 413 CONECT 458 467 CONECT 467 458 CONECT 469 470 471 472 CONECT 470 469 CONECT 471 469 CONECT 472 469 CONECT 474 489 CONECT 483 484 487 CONECT 484 483 488 CONECT 485 486 487 500 CONECT 486 485 488 CONECT 487 483 485 CONECT 488 484 486 CONECT 489 474 490 CONECT 490 489 491 493 CONECT 491 490 492 502 CONECT 492 491 CONECT 493 490 494 CONECT 494 493 495 496 CONECT 495 494 497 CONECT 496 494 498 CONECT 497 495 499 CONECT 498 496 499 CONECT 499 497 498 501 CONECT 500 485 501 CONECT 501 499 500 CONECT 502 491 CONECT 536 545 CONECT 545 536 MASTER 136 0 21 0 0 0 0 6 557 7 189 7 END