HEADER PROTEIN FIBRIL 10-DEC-24 9MGA TITLE CRYO-EM OF 3-PROTOFILAMENT HELICAL FIBERS FORMED BY (NAP)FFGPQYQP COMPND MOL_ID: 1; COMPND 2 MOLECULE: (I7L)FFGPQYQP; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PEPTIDE FIBER, HELICAL POLYMER, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR A.ZIA,Y.QIAO,B.XU,F.WANG REVDAT 3 09-JUL-25 9MGA 1 JRNL REVDAT 2 14-MAY-25 9MGA 1 JRNL REVDAT 1 07-MAY-25 9MGA 0 JRNL AUTH Y.QIAO,A.ZIA,A.SHY,G.WU,M.CHU,Z.LIU,F.WANG,B.XU JRNL TITL INTRINSICALLY DISORDERED PEPTIDE NANOFIBERS FROM A JRNL TITL 2 STRUCTURED MOTIF WITHIN PROTEINS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 64 25456 2025 JRNL REFN ESSN 1521-3773 JRNL PMID 40294067 JRNL DOI 10.1002/ANIE.202425456 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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) : 2.850 REMARK 3 NUMBER OF PARTICLES : 160380 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 9MGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1000290915. 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 : (I7L)FFGPQYQP 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -120.70 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 1.70 ANGSTROMS 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 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 BIOMT1 2 -0.510543 -0.859852 0.000000 421.40300 REMARK 350 BIOMT2 2 0.859852 -0.510543 0.000000 115.83400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -1.70000 REMARK 350 BIOMT1 3 -0.510543 0.859852 0.000000 115.54400 REMARK 350 BIOMT2 3 -0.859852 -0.510543 0.000000 421.48200 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 1.70000 REMARK 350 BIOMT1 4 -0.478692 -0.877983 0.000000 418.96700 REMARK 350 BIOMT2 4 0.877983 -0.478692 0.000000 106.94600 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 3.40000 REMARK 350 BIOMT1 5 0.999328 0.036644 0.000000 -6.39791 REMARK 350 BIOMT2 5 -0.036644 0.999328 0.000000 6.63225 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 5.10000 REMARK 350 BIOMT1 6 -0.541708 0.840567 0.000000 124.51400 REMARK 350 BIOMT2 6 -0.840567 -0.541708 0.000000 423.59800 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 6.80000 REMARK 350 BIOMT1 7 -0.446198 -0.894934 0.000000 416.20600 REMARK 350 BIOMT2 7 0.894934 -0.446198 0.000000 98.15440 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 8.50000 REMARK 350 BIOMT1 8 0.997314 0.073238 0.000000 -12.54850 REMARK 350 BIOMT2 8 -0.073238 0.997314 0.000000 13.49450 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 10.20000 REMARK 350 BIOMT1 9 -0.572146 0.820152 0.000000 133.55400 REMARK 350 BIOMT2 9 -0.820152 -0.572146 0.000000 425.38300 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 11.90000 REMARK 350 BIOMT1 10 -0.413104 -0.910684 0.000000 413.12500 REMARK 350 BIOMT2 10 0.910684 -0.413104 0.000000 89.46940 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 13.60000 REMARK 350 BIOMT1 11 0.993961 0.109734 0.000000 -18.44350 REMARK 350 BIOMT2 11 -0.109734 0.993961 0.000000 20.57750 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 15.30000 REMARK 350 BIOMT1 12 -0.601815 0.798636 0.000000 142.65400 REMARK 350 BIOMT2 12 -0.798636 -0.601815 0.000000 426.83500 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 17.00000 REMARK 350 BIOMT1 13 -0.379456 -0.925210 0.000000 409.72900 REMARK 350 BIOMT2 13 0.925210 -0.379456 0.000000 80.90310 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 18.70000 REMARK 350 BIOMT1 14 0.989272 0.146083 0.000000 -24.07500 REMARK 350 BIOMT2 14 -0.146083 0.989272 0.000000 27.87180 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 20.40000 REMARK 350 BIOMT1 15 -0.630676 0.776046 0.000000 151.80100 REMARK 350 BIOMT2 15 -0.776046 -0.630676 0.000000 427.95400 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 22.10000 REMARK 350 BIOMT1 16 -0.345298 -0.938493 0.000000 406.02000 REMARK 350 BIOMT2 16 0.938493 -0.345298 0.000000 72.46700 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 23.80000 REMARK 350 BIOMT1 17 0.983255 0.182236 0.000000 -29.43540 REMARK 350 BIOMT2 17 -0.182236 0.983255 0.000000 35.36750 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 25.50000 REMARK 350 BIOMT1 18 -0.658689 0.752415 0.000000 160.98300 REMARK 350 BIOMT2 18 -0.752415 -0.658689 0.000000 428.73600 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 27.20000 REMARK 350 BIOMT1 19 -0.310676 -0.950516 0.000000 402.00500 REMARK 350 BIOMT2 19 0.950516 -0.310676 0.000000 64.17250 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 28.90000 REMARK 350 BIOMT1 20 0.975917 0.218143 0.000000 -34.51750 REMARK 350 BIOMT2 20 -0.218143 0.975917 0.000000 43.05460 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 30.60000 REMARK 350 BIOMT1 21 -0.685818 0.727773 0.000000 170.18800 REMARK 350 BIOMT2 21 -0.727773 -0.685818 0.000000 429.18100 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 32.30000 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 GLN A 8 REMARK 465 PRO A 9 REMARK 465 PRO B 9 REMARK 465 PRO C 9 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48244 RELATED DB: EMDB REMARK 900 CRYO-EM OF 3-PROTOFILAMENT HELICAL FIBERS FORMED BY (NAP)FFGPQYQP DBREF 9MGA A 1 9 PDB 9MGA 9MGA 1 9 DBREF 9MGA B 1 9 PDB 9MGA 9MGA 1 9 DBREF 9MGA C 1 9 PDB 9MGA 9MGA 1 9 SEQRES 1 A 9 I7L PHE PHE GLY PRO GLN TYR GLN PRO SEQRES 1 B 9 I7L PHE PHE GLY PRO GLN TYR GLN PRO SEQRES 1 C 9 I7L PHE PHE GLY PRO GLN TYR GLN PRO HET I7L A 1 13 HET I7L B 1 13 HET I7L C 1 13 HETNAM I7L 2-NAPHTHALEN-2-YLETHANOIC ACID FORMUL 1 I7L 3(C12 H10 O2) LINK C02 I7L A 1 N PHE A 2 1555 1555 1.41 LINK C02 I7L B 1 N PHE B 2 1555 1555 1.41 LINK C02 I7L C 1 N PHE C 2 1555 1555 1.41 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 CONECT 1 10 11 CONECT 2 9 12 13 CONECT 3 4 CONECT 4 3 5 14 CONECT 5 4 6 CONECT 6 5 7 13 CONECT 7 6 8 CONECT 8 7 9 CONECT 9 2 8 10 CONECT 10 1 9 CONECT 11 1 12 CONECT 12 2 11 CONECT 13 2 6 CONECT 14 4 CONECT 69 78 79 CONECT 70 77 80 81 CONECT 71 72 CONECT 72 71 73 82 CONECT 73 72 74 CONECT 74 73 75 81 CONECT 75 74 76 CONECT 76 75 77 CONECT 77 70 76 78 CONECT 78 69 77 CONECT 79 69 80 CONECT 80 70 79 CONECT 81 70 74 CONECT 82 72 CONECT 146 155 156 CONECT 147 154 157 158 CONECT 148 149 CONECT 149 148 150 159 CONECT 150 149 151 CONECT 151 150 152 158 CONECT 152 151 153 CONECT 153 152 154 CONECT 154 147 153 155 CONECT 155 146 154 CONECT 156 146 157 CONECT 157 147 156 CONECT 158 147 151 CONECT 159 149 MASTER 171 0 3 0 0 0 0 6 219 3 42 3 END