HEADER PROTEIN FIBRIL 20-FEB-25 9NET TITLE CRYO-EM OF NBD-L4PY FILAMENT AT 0.4 MM CONCENTRATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: (UQ4)LLLL(PTR); COMPND 3 CHAIN: A; 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,J.GUO,B.XU,F.WANG REVDAT 1 11-MAR-26 9NET 0 JRNL AUTH A.ZIA,J.GUO,B.XU,F.WANG JRNL TITL CRYO-EM OF NBD-L4PY FILAMENT AT 0.4 MM CONCENTRATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.50 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 218959 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 9NET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293193. 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 : (UQ4)LLLL(PTR) 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) = 4.05 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 4.80 ANGSTROMS REMARK 300 IN ADDITION, THERE IS 1313-FOLD CIRCULAR REMARK 300 SYMMETRY AROUND THE HELIX AXIS 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 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 0.990024 0.140901 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.140901 0.990024 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 3 0.997503 0.070627 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.070627 0.997503 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 4 0.997503 -0.070627 0.000000 0.00000 REMARK 350 BIOMT2 4 0.070627 0.997503 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 5 0.942102 -0.335325 0.000000 0.00000 REMARK 350 BIOMT2 5 0.335325 0.942102 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 6 0.916067 -0.401026 0.000000 0.00000 REMARK 350 BIOMT2 6 0.401026 0.916067 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 7 0.885456 -0.464723 0.000000 0.00000 REMARK 350 BIOMT2 7 0.464723 0.885456 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 0.850423 -0.526100 0.000000 0.00000 REMARK 350 BIOMT2 8 0.526100 0.850423 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 9 0.678357 -0.734732 0.000000 0.00000 REMARK 350 BIOMT2 9 0.734732 0.678357 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 10 0.624771 -0.780808 0.000000 0.00000 REMARK 350 BIOMT2 10 0.780808 0.624771 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 11 0.568065 -0.822984 0.000000 0.00000 REMARK 350 BIOMT2 11 0.822984 0.568065 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 12 0.508521 -0.861049 0.000000 0.00000 REMARK 350 BIOMT2 12 0.861049 0.508521 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 13 0.259208 -0.965822 0.000000 0.00000 REMARK 350 BIOMT2 13 0.965822 0.259208 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 14 0.190348 -0.981717 0.000000 0.00000 REMARK 350 BIOMT2 14 0.981717 0.190348 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 15 0.120537 -0.992709 0.000000 0.00000 REMARK 350 BIOMT2 15 0.992709 0.120537 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 16 0.050124 -0.998743 0.000000 0.00000 REMARK 350 BIOMT2 16 0.998743 0.050124 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 17 -0.219322 -0.975652 0.000000 0.00000 REMARK 350 BIOMT2 17 0.975652 -0.219322 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 18 -0.287682 -0.957726 0.000000 0.00000 REMARK 350 BIOMT2 18 0.957726 -0.287682 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 19 -0.354605 -0.935016 0.000000 0.00000 REMARK 350 BIOMT2 19 0.935016 -0.354605 0.000000 0.00000 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 20 -0.419757 -0.907637 0.000000 0.00000 REMARK 350 BIOMT2 20 0.907637 -0.419757 0.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 21 -0.647609 -0.761973 0.000000 0.00000 REMARK 350 BIOMT2 21 0.761973 -0.647609 0.000000 0.00000 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 22 -0.699807 -0.714332 0.000000 0.00000 REMARK 350 BIOMT2 22 0.714332 -0.699807 0.000000 0.00000 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 23 -0.748511 -0.663123 0.000000 0.00000 REMARK 350 BIOMT2 23 0.663123 -0.748511 0.000000 0.00000 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 24 -0.793476 -0.608602 0.000000 0.00000 REMARK 350 BIOMT2 24 0.608602 -0.793476 0.000000 0.00000 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 25 -0.927535 -0.373735 0.000000 0.00000 REMARK 350 BIOMT2 25 0.373735 -0.927535 0.000000 0.00000 REMARK 350 BIOMT3 25 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 26 -0.951615 -0.307293 0.000000 0.00000 REMARK 350 BIOMT2 26 0.307293 -0.951615 0.000000 0.00000 REMARK 350 BIOMT3 26 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 27 -0.970942 -0.239316 0.000000 0.00000 REMARK 350 BIOMT2 27 0.239316 -0.970942 0.000000 0.00000 REMARK 350 BIOMT3 27 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 28 -0.985419 -0.170143 0.000000 0.00000 REMARK 350 BIOMT2 28 0.170143 -0.985419 0.000000 0.00000 REMARK 350 BIOMT3 28 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 29 -0.994975 0.100121 0.000000 0.00000 REMARK 350 BIOMT2 29 -0.100121 -0.994975 0.000000 0.00000 REMARK 350 BIOMT3 29 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 30 -0.985419 0.170143 0.000000 0.00000 REMARK 350 BIOMT2 30 -0.170143 -0.985419 0.000000 0.00000 REMARK 350 BIOMT3 30 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 31 -0.970942 0.239316 0.000000 0.00000 REMARK 350 BIOMT2 31 -0.239316 -0.970942 0.000000 0.00000 REMARK 350 BIOMT3 31 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 32 -0.951615 0.307293 0.000000 0.00000 REMARK 350 BIOMT2 32 -0.307293 -0.951615 0.000000 0.00000 REMARK 350 BIOMT3 32 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 33 -0.834478 0.551041 0.000000 0.00000 REMARK 350 BIOMT2 33 -0.551041 -0.834478 0.000000 0.00000 REMARK 350 BIOMT3 33 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 34 -0.793476 0.608602 0.000000 0.00000 REMARK 350 BIOMT2 34 -0.608602 -0.793476 0.000000 0.00000 REMARK 350 BIOMT3 34 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 35 -0.748511 0.663123 0.000000 0.00000 REMARK 350 BIOMT2 35 -0.663123 -0.748511 0.000000 0.00000 REMARK 350 BIOMT3 35 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 36 -0.699807 0.714332 0.000000 0.00000 REMARK 350 BIOMT2 36 -0.714332 -0.699807 0.000000 0.00000 REMARK 350 BIOMT3 36 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 37 -0.482812 0.875724 0.000000 0.00000 REMARK 350 BIOMT2 37 -0.875724 -0.482812 0.000000 0.00000 REMARK 350 BIOMT3 37 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 38 -0.419757 0.907637 0.000000 0.00000 REMARK 350 BIOMT2 38 -0.907637 -0.419757 0.000000 0.00000 REMARK 350 BIOMT3 38 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 39 -0.354605 0.935016 0.000000 0.00000 REMARK 350 BIOMT2 39 -0.935016 -0.354605 0.000000 0.00000 REMARK 350 BIOMT3 39 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 40 -0.287682 0.957726 0.000000 0.00000 REMARK 350 BIOMT2 40 -0.957726 -0.287682 0.000000 0.00000 REMARK 350 BIOMT3 40 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 41 -0.020540 0.999789 0.000000 0.00000 REMARK 350 BIOMT2 41 -0.999789 -0.020540 0.000000 0.00000 REMARK 350 BIOMT3 41 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 42 0.050124 0.998743 0.000000 0.00000 REMARK 350 BIOMT2 42 -0.998743 0.050124 0.000000 0.00000 REMARK 350 BIOMT3 42 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 43 0.120537 0.992709 0.000000 0.00000 REMARK 350 BIOMT2 43 -0.992709 0.120537 0.000000 0.00000 REMARK 350 BIOMT3 43 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 44 0.190348 0.981717 0.000000 0.00000 REMARK 350 BIOMT2 44 -0.981717 0.190348 0.000000 0.00000 REMARK 350 BIOMT3 44 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 45 0.446438 0.894815 0.000000 0.00000 REMARK 350 BIOMT2 45 -0.894815 0.446438 0.000000 0.00000 REMARK 350 BIOMT3 45 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 46 0.508521 0.861049 0.000000 0.00000 REMARK 350 BIOMT2 46 -0.861049 0.508521 0.000000 0.00000 REMARK 350 BIOMT3 46 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 47 0.568065 0.822984 0.000000 0.00000 REMARK 350 BIOMT2 47 -0.822984 0.568065 0.000000 0.00000 REMARK 350 BIOMT3 47 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 48 0.624771 0.780808 0.000000 0.00000 REMARK 350 BIOMT2 48 -0.780808 0.624771 0.000000 0.00000 REMARK 350 BIOMT3 48 0.000000 0.000000 1.000000 4.80000 REMARK 350 BIOMT1 49 0.811142 0.584849 0.000000 0.00000 REMARK 350 BIOMT2 49 -0.584849 0.811142 0.000000 0.00000 REMARK 350 BIOMT3 49 0.000000 0.000000 1.000000 -9.60000 REMARK 350 BIOMT1 50 0.850423 0.526100 0.000000 0.00000 REMARK 350 BIOMT2 50 -0.526100 0.850423 0.000000 0.00000 REMARK 350 BIOMT3 50 0.000000 0.000000 1.000000 -4.80000 REMARK 350 BIOMT1 51 0.885456 0.464723 0.000000 0.00000 REMARK 350 BIOMT2 51 -0.464723 0.885456 0.000000 0.00000 REMARK 350 BIOMT3 51 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 52 0.916067 0.401026 0.000000 0.00000 REMARK 350 BIOMT2 52 -0.401026 0.916067 0.000000 0.00000 REMARK 350 BIOMT3 52 0.000000 0.000000 1.000000 4.80000 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49335 RELATED DB: EMDB REMARK 900 CRYO-EM OF NBD-L4PY FILAMENT AT 0.4 MM CONCENTRATION DBREF 9NET A 1 6 PDB 9NET 9NET 1 6 SEQRES 1 A 6 UQ4 LEU LEU LEU LEU PTR HET UQ4 A 1 17 HET PTR A 6 17 HETNAM UQ4 N-(7-NITRO-2,1,3-BENZOXADIAZOL-4-YL)-BETA-ALANINE HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 UQ4 C9 H8 N4 O5 FORMUL 1 PTR C9 H12 N O6 P LINK C02 UQ4 A 1 N LEU A 2 1555 1555 1.32 LINK C LEU A 5 N PTR A 6 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 14 18 CONECT 2 1 3 CONECT 3 2 10 CONECT 4 5 9 10 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 6 8 11 CONECT 8 7 9 12 CONECT 9 4 8 13 CONECT 10 3 4 CONECT 11 7 15 16 CONECT 12 8 17 CONECT 13 9 17 CONECT 14 1 CONECT 15 11 CONECT 16 11 CONECT 17 12 13 CONECT 18 1 CONECT 44 50 CONECT 50 44 51 CONECT 51 50 52 55 CONECT 52 51 53 54 CONECT 53 52 CONECT 54 52 CONECT 55 51 56 CONECT 56 55 57 58 CONECT 57 56 59 CONECT 58 56 60 CONECT 59 57 61 CONECT 60 58 61 CONECT 61 59 60 62 CONECT 62 61 63 CONECT 63 62 64 65 66 CONECT 64 63 CONECT 65 63 CONECT 66 63 MASTER 255 0 2 0 0 0 0 6 66 1 36 1 END