HEADER PROTEIN FIBRIL 12-MAR-25 9QFM TITLE LY12 MAIN MORPHOLOGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 12S SEED STORAGE PROTEIN CRC ALPHA CHAIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, a, b, c, d, e, f, g, h, i, j, k, COMPND 4 l, m, n, o, p, q, r, s, t, u, v, w, x, y, z; COMPND 5 SYNONYM: 12S SEED STORAGE PROTEIN CRC ACIDIC CHAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 4 ORGANISM_COMMON: THALE CRESS; SOURCE 5 ORGANISM_TAXID: 3702 KEYWDS AMYLOID FIBRIL, SEED STORAGE PROTEIN, IN VITRO, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR N.STOYANOV,M.SCHMIDT,M.FAENDRICH REVDAT 1 15-APR-26 9QFM 0 JRNL AUTH V.KUMAR,N.STOYANOV,V.KAUSHIK,S.KUMAR,M.SCHMIDT,M.FANDRICH, JRNL AUTH 2 D.SEGAL JRNL TITL A FRAGMENT OF 12S SEED STORAGE PROTEIN OF ARABIDOPSIS FORMS JRNL TITL 2 TWISTED CROSS BETA-SHEET RICH AMYLOID FIBRILS. JRNL REF INT.J.BIOL.MACROMOL. 51751 2026 JRNL REFN ISSN 0141-8130 JRNL PMID 41932473 JRNL DOI 10.1016/J.IJBIOMAC.2026.151751 REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, RELION, RELION, RELION, RELION, REMARK 3 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 : AB INITIO MODEL 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) : 2.960 REMARK 3 NUMBER OF PARTICLES : 134959 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 9QFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292145376. 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 : AMYLOID FIBRIL FORMED BY THE REMARK 245 AGGREGATION OF A 12 AA LONG REMARK 245 FRAGMENT FROM CRUCIFERIN 3 (223- REMARK 245 234) FROM A. THALIANA. 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 : 7.20 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) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5229.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 165000 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: 36-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 36-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: a, b, c, d, e, f, g, h, i, REMARK 350 AND CHAINS: j, k, l, m, n, o, p, q, r, s, REMARK 350 AND CHAINS: t, u, v, w, x, y, z REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN B 233 REMARK 465 TYR B 234 REMARK 465 ASN C 233 REMARK 465 TYR C 234 REMARK 465 ASN G 233 REMARK 465 TYR G 234 REMARK 465 ASN J 233 REMARK 465 TYR J 234 REMARK 465 ASN b 233 REMARK 465 TYR b 234 REMARK 465 ASN f 233 REMARK 465 TYR f 234 REMARK 465 ASN i 233 REMARK 465 TYR i 234 REMARK 465 ASN l 233 REMARK 465 TYR l 234 REMARK 465 ASN o 233 REMARK 465 TYR o 234 REMARK 465 ASN r 233 REMARK 465 TYR r 234 REMARK 465 ASN u 233 REMARK 465 TYR u 234 REMARK 465 ASN x 233 REMARK 465 TYR x 234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-53117 RELATED DB: EMDB REMARK 900 LY12 MAIN MORPHOLOGY DBREF 9QFM A 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM B 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM C 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM D 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM E 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM F 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM G 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM H 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM I 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM J 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM a 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM b 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM c 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM d 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM e 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM f 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM g 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM h 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM i 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM j 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM k 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM l 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM m 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM n 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM o 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM p 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM q 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM r 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM s 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM t 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM u 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM v 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM w 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM x 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM y 223 234 UNP Q96318 CRU3_ARATH 223 234 DBREF 9QFM z 223 234 UNP Q96318 CRU3_ARATH 223 234 SEQRES 1 A 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 B 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 C 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 D 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 E 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 F 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 G 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 H 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 I 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 J 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 a 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 b 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 c 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 d 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 e 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 f 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 g 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 h 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 i 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 j 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 k 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 l 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 m 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 n 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 o 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 p 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 q 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 r 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 s 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 t 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 u 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 v 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 w 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 x 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 y 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SEQRES 1 z 12 LEU VAL ILE ILE ALA LEU LEU ASP ILE ALA ASN TYR SHEET 1 AA1 6 VAL F 224 ILE F 225 0 SHEET 2 AA1 6 VAL A 224 ILE A 225 1 N ILE A 225 O VAL F 224 SHEET 3 AA1 6 VAL t 224 ILE t 225 1 O ILE t 225 N VAL A 224 SHEET 4 AA1 6 VAL n 224 ILE n 225 1 N ILE n 225 O VAL t 224 SHEET 5 AA1 6 VAL h 224 ILE h 225 1 N ILE h 225 O VAL n 224 SHEET 6 AA1 6 VAL a 224 ILE a 225 1 N ILE a 225 O VAL h 224 SHEET 1 AA2 6 LEU F 228 ASN F 233 0 SHEET 2 AA2 6 LEU A 228 ASN A 233 1 N ALA A 232 O ILE F 231 SHEET 3 AA2 6 LEU t 228 ASN t 233 1 O ALA t 232 N ILE A 231 SHEET 4 AA2 6 LEU n 228 ASN n 233 1 N ALA n 232 O ILE t 231 SHEET 5 AA2 6 LEU h 228 ASN h 233 1 N ALA h 232 O ILE n 231 SHEET 6 AA2 6 LEU a 228 ASN a 233 1 N ALA a 232 O ILE h 231 SHEET 1 AA3 6 VAL G 224 ASP G 230 0 SHEET 2 AA3 6 VAL B 224 ASP B 230 1 N ILE B 226 O ILE G 225 SHEET 3 AA3 6 VAL u 224 ASP u 230 1 O ILE u 226 N ILE B 225 SHEET 4 AA3 6 VAL o 224 ASP o 230 1 N ILE o 226 O ILE u 225 SHEET 5 AA3 6 VAL i 224 ASP i 230 1 N ILE i 226 O ILE o 225 SHEET 6 AA3 6 VAL b 224 ASP b 230 1 N ILE b 226 O ILE i 225 SHEET 1 AA4 6 VAL J 224 ASP J 230 0 SHEET 2 AA4 6 VAL C 224 ASP C 230 1 N ILE C 226 O ILE J 225 SHEET 3 AA4 6 VAL x 224 ASP x 230 1 O ILE x 226 N ILE C 225 SHEET 4 AA4 6 VAL r 224 ASP r 230 1 N ILE r 226 O ILE x 225 SHEET 5 AA4 6 VAL l 224 ASP l 230 1 N ILE l 226 O ILE r 225 SHEET 6 AA4 6 VAL f 224 ASP f 230 1 N ILE f 226 O ILE l 225 SHEET 1 AA5 6 VAL H 224 LEU H 229 0 SHEET 2 AA5 6 VAL D 224 LEU D 229 1 N ALA D 227 O LEU H 228 SHEET 3 AA5 6 VAL v 224 LEU v 229 1 O ALA v 227 N LEU D 228 SHEET 4 AA5 6 VAL p 224 LEU p 229 1 N ALA p 227 O LEU v 228 SHEET 5 AA5 6 VAL j 224 LEU j 229 1 N ALA j 227 O LEU p 228 SHEET 6 AA5 6 VAL d 224 LEU d 229 1 N ALA d 227 O LEU j 228 SHEET 1 AA6 6 ALA H 232 ASN H 233 0 SHEET 2 AA6 6 ALA D 232 ASN D 233 1 N ASN D 233 O ALA H 232 SHEET 3 AA6 6 ALA v 232 ASN v 233 1 O ASN v 233 N ALA D 232 SHEET 4 AA6 6 ALA p 232 ASN p 233 1 N ASN p 233 O ALA v 232 SHEET 5 AA6 6 ALA j 232 ASN j 233 1 N ASN j 233 O ALA p 232 SHEET 6 AA6 6 ALA d 232 ASN d 233 1 N ASN d 233 O ALA j 232 SHEET 1 AA7 6 VAL I 224 ILE I 225 0 SHEET 2 AA7 6 VAL E 224 ILE E 225 1 N ILE E 225 O VAL I 224 SHEET 3 AA7 6 VAL w 224 ILE w 225 1 O ILE w 225 N VAL E 224 SHEET 4 AA7 6 VAL q 224 ILE q 225 1 N ILE q 225 O VAL w 224 SHEET 5 AA7 6 VAL k 224 ILE k 225 1 N ILE k 225 O VAL q 224 SHEET 6 AA7 6 VAL e 224 ILE e 225 1 N ILE e 225 O VAL k 224 SHEET 1 AA8 6 LEU I 228 ASN I 233 0 SHEET 2 AA8 6 LEU E 228 ASN E 233 1 N ALA E 232 O ILE I 231 SHEET 3 AA8 6 LEU w 228 ASN w 233 1 O ALA w 232 N ILE E 231 SHEET 4 AA8 6 LEU q 228 ASN q 233 1 N ALA q 232 O ILE w 231 SHEET 5 AA8 6 LEU k 228 ASN k 233 1 N ALA k 232 O ILE q 231 SHEET 6 AA8 6 LEU e 228 ASN e 233 1 N ALA e 232 O ILE k 231 SHEET 1 AA9 6 VAL c 224 LEU c 229 0 SHEET 2 AA9 6 VAL z 224 LEU z 229 1 O ALA z 227 N LEU c 228 SHEET 3 AA9 6 VAL y 224 LEU y 229 1 N ALA y 227 O LEU z 228 SHEET 4 AA9 6 VAL s 224 LEU s 229 1 N ALA s 227 O LEU y 228 SHEET 5 AA9 6 VAL m 224 LEU m 229 1 N ALA m 227 O LEU s 228 SHEET 6 AA9 6 VAL g 224 LEU g 229 1 N ALA g 227 O LEU m 228 SHEET 1 AB1 6 ALA c 232 ASN c 233 0 SHEET 2 AB1 6 ALA z 232 ASN z 233 1 O ASN z 233 N ALA c 232 SHEET 3 AB1 6 ALA y 232 ASN y 233 1 N ASN y 233 O ALA z 232 SHEET 4 AB1 6 ALA s 232 ASN s 233 1 N ASN s 233 O ALA y 232 SHEET 5 AB1 6 ALA m 232 ASN m 233 1 N ASN m 233 O ALA s 232 SHEET 6 AB1 6 ALA g 232 ASN g 233 1 N ASN g 233 O ALA m 232 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MASTER 137 0 0 0 60 0 0 6 3132 36 0 36 END