HEADER PROTEIN FIBRIL 20-FEB-25 9NEQ TITLE CRYO-EM OF NBD-L4PY NANOFIBERS AT 1.25MM CONCENTRATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: (UQ4)LLLL(PTR); 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,J.GUO,B.XU,F.WANG REVDAT 1 11-MAR-26 9NEQ 0 JRNL AUTH A.ZIA,J.GUO,B.XU,F.WANG JRNL TITL CRYO-EM OF NBD-L4PY NANOFIBERS AT 1.25MM 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 : 881591 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 9NEQ 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_1000293214. 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) = 4.01 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 4.66 ANGSTROMS REMARK 300 IN ADDITION, THERE IS 2-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, 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 0.990219 0.139519 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.139519 0.990219 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -9.32000 REMARK 350 BIOMT1 3 0.997552 0.069931 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.069931 0.997552 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -4.66000 REMARK 350 BIOMT1 4 0.997552 -0.069931 0.000000 0.00000 REMARK 350 BIOMT2 4 0.069931 0.997552 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 4.66000 REMARK 350 BIOMT1 5 -0.990219 -0.139519 0.000000 0.00000 REMARK 350 BIOMT2 5 0.139519 -0.990219 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -9.32000 REMARK 350 BIOMT1 6 -0.997552 -0.069931 0.000000 0.00000 REMARK 350 BIOMT2 6 0.069931 -0.997552 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -4.66000 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 -0.997552 0.069931 0.000000 0.00000 REMARK 350 BIOMT2 8 -0.069931 -0.997552 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 4.66000 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 PTR A 6 REMARK 465 PTR B 6 REMARK 465 PTR C 6 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 UQ4 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-49330 RELATED DB: EMDB REMARK 900 CRYO-EM OF NBD-L4PY NANOFIBERS AT 1.25MM CONCENTRATION DBREF 9NEQ A 1 6 PDB 9NEQ 9NEQ 1 6 DBREF 9NEQ B 1 6 PDB 9NEQ 9NEQ 1 6 DBREF 9NEQ C 1 6 PDB 9NEQ 9NEQ 1 6 SEQRES 1 A 6 UQ4 LEU LEU LEU LEU PTR SEQRES 1 B 6 UQ4 LEU LEU LEU LEU PTR SEQRES 1 C 6 UQ4 LEU LEU LEU LEU PTR HET UQ4 A 1 17 HET UQ4 B 1 17 HET UQ4 C 1 17 HET UQ4 B 101 17 HETNAM UQ4 N-(7-NITRO-2,1,3-BENZOXADIAZOL-4-YL)-BETA-ALANINE FORMUL 1 UQ4 4(C9 H8 N4 O5) LINK C02 UQ4 A 1 N LEU A 2 1555 1555 1.33 LINK C02 UQ4 B 1 N LEU B 2 1555 1555 1.33 LINK C02 UQ4 C 1 N LEU C 2 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 51 52 64 68 CONECT 52 51 53 CONECT 53 52 60 CONECT 54 55 59 60 CONECT 55 54 56 CONECT 56 55 57 CONECT 57 56 58 61 CONECT 58 57 59 62 CONECT 59 54 58 63 CONECT 60 53 54 CONECT 61 57 65 66 CONECT 62 58 67 CONECT 63 59 67 CONECT 64 51 CONECT 65 61 CONECT 66 61 CONECT 67 62 63 CONECT 68 51 CONECT 101 102 114 118 CONECT 102 101 103 CONECT 103 102 110 CONECT 104 105 109 110 CONECT 105 104 106 CONECT 106 105 107 CONECT 107 106 108 111 CONECT 108 107 109 112 CONECT 109 104 108 113 CONECT 110 103 104 CONECT 111 107 115 116 CONECT 112 108 117 CONECT 113 109 117 CONECT 114 101 CONECT 115 111 CONECT 116 111 CONECT 117 112 113 CONECT 118 101 CONECT 151 152 164 CONECT 152 151 153 CONECT 153 152 160 CONECT 154 155 159 160 CONECT 155 154 156 CONECT 156 155 157 CONECT 157 156 158 161 CONECT 158 157 159 162 CONECT 159 154 158 163 CONECT 160 153 154 CONECT 161 157 165 166 CONECT 162 158 167 CONECT 163 159 167 CONECT 164 151 CONECT 165 161 CONECT 166 161 CONECT 167 162 163 MASTER 140 0 4 0 0 0 0 6 164 3 71 3 END