HEADER PROTEIN FIBRIL 02-AUG-24 9J0M TITLE CRYO-EM STRUCTURE OF LYSOZYME TYPE 2 AMYLOID FIBRILS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 5 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS AMYLOID, FIBRIL, LYSOZYME, HEN EGG WHITE LYSOZYME, HEWL, PROTEIN KEYWDS 2 FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR H.KAWABATA,S.Y.PARK REVDAT 1 06-AUG-25 9J0M 0 JRNL AUTH H.KAWABATA,Y.LI,H.UMEZAWA,Y.LIN,N.ISHIMOTO,Y.YUN,Y.HEO, JRNL AUTH 2 J.H.PARK,Y.H.LEE,S.Y.PARK JRNL TITL STRUCTURAL BASIS FOR AMYLOID FIBRIL FORMATION BY LYSOZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU 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) : 3.210 REMARK 3 NUMBER OF PARTICLES : 1 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 9J0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300049684. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : HEN EGG WHITE LYSOZYME (HEWL) REMARK 245 AMYLOID REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 5.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 2.00 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: 16-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 -0.999945 0.010524 0.000000 277.96286 REMARK 350 BIOMT2 1 -0.010524 -0.999945 0.000000 280.90374 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -7.15005 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.999975 -0.007016 0.000000 0.98374 REMARK 350 BIOMT2 3 0.007016 0.999975 0.000000 -0.97686 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -4.76670 REMARK 350 BIOMT1 4 -0.999994 0.003508 0.000000 278.95003 REMARK 350 BIOMT2 4 -0.003508 -0.999994 0.000000 279.93033 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -2.38335 REMARK 350 BIOMT1 5 -0.999994 -0.003508 0.000000 279.93033 REMARK 350 BIOMT2 5 0.003508 -0.999994 0.000000 278.95003 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 2.38335 REMARK 350 BIOMT1 6 0.999975 0.007016 0.000000 -0.97686 REMARK 350 BIOMT2 6 -0.007016 0.999975 0.000000 0.98374 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 4.76670 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 0.999975 -0.007016 0.000000 0.98374 REMARK 350 BIOMT2 8 0.007016 0.999975 0.000000 -0.97686 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -4.76670 REMARK 350 BIOMT1 9 -0.999994 0.003508 0.000000 278.95003 REMARK 350 BIOMT2 9 -0.003508 -0.999994 0.000000 279.93033 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -2.38335 REMARK 350 BIOMT1 10 -0.999994 -0.003508 0.000000 279.93033 REMARK 350 BIOMT2 10 0.003508 -0.999994 0.000000 278.95003 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 2.38335 REMARK 350 BIOMT1 11 0.999975 0.007016 0.000000 -0.97686 REMARK 350 BIOMT2 11 -0.007016 0.999975 0.000000 0.98374 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 4.76670 REMARK 350 BIOMT1 12 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 12 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 13 0.999975 -0.007016 0.000000 0.98374 REMARK 350 BIOMT2 13 0.007016 0.999975 0.000000 -0.97686 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -4.76670 REMARK 350 BIOMT1 14 -0.999994 0.003508 0.000000 278.95003 REMARK 350 BIOMT2 14 -0.003508 -0.999994 0.000000 279.93033 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -2.38335 REMARK 350 BIOMT1 15 -0.999994 -0.003508 0.000000 279.93033 REMARK 350 BIOMT2 15 0.003508 -0.999994 0.000000 278.95003 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 2.38335 REMARK 350 BIOMT1 16 0.999975 0.007016 0.000000 -0.97686 REMARK 350 BIOMT2 16 -0.007016 0.999975 0.000000 0.98374 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 4.76670 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 17 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 17 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 18 0.999975 -0.007016 0.000000 0.98374 REMARK 350 BIOMT2 18 0.007016 0.999975 0.000000 -0.97686 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 -4.76670 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 19 -0.999994 0.003508 0.000000 278.95003 REMARK 350 BIOMT2 19 -0.003508 -0.999994 0.000000 279.93033 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 -2.38335 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 20 -0.999994 -0.003508 0.000000 279.93033 REMARK 350 BIOMT2 20 0.003508 -0.999994 0.000000 278.95003 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 2.38335 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 21 0.999975 0.007016 0.000000 -0.97686 REMARK 350 BIOMT2 21 -0.007016 0.999975 0.000000 0.98374 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 4.76670 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 30 47.39 76.94 REMARK 500 ALA A 32 -132.80 -116.88 REMARK 500 TRP A 63 -145.41 -91.44 REMARK 500 ASN A 74 61.87 62.89 REMARK 500 ALA A 110 60.59 65.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TRP A 63 CYS A 64 -149.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 21 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-61057 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF LYSOZYME AMYLOID FIBRIL, TYPE 2 DBREF 9J0M A 5 129 UNP P00698 LYSC_CHICK 23 147 SEQRES 1 A 125 ARG CYS GLU LEU ALA ALA ALA MET LYS ARG HIS GLY LEU SEQRES 2 A 125 ASP ASN TYR ARG GLY TYR SER LEU GLY ASN TRP VAL CYS SEQRES 3 A 125 ALA ALA LYS PHE GLU SER ASN PHE ASN THR GLN ALA THR SEQRES 4 A 125 ASN ARG ASN THR ASP GLY SER THR ASP TYR GLY ILE LEU SEQRES 5 A 125 GLN ILE ASN SER ARG TRP TRP CYS ASN ASP GLY ARG THR SEQRES 6 A 125 PRO GLY SER ARG ASN LEU CYS ASN ILE PRO CYS SER ALA SEQRES 7 A 125 LEU LEU SER SER ASP ILE THR ALA SER VAL ASN CYS ALA SEQRES 8 A 125 LYS LYS ILE VAL SER ASP GLY ASN GLY MET ASN ALA TRP SEQRES 9 A 125 VAL ALA TRP ARG ASN ARG CYS LYS GLY THR ASP VAL GLN SEQRES 10 A 125 ALA TRP ILE ARG GLY CYS ARG LEU SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.04 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.05 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.01 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.02 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 MTRIX1 50 0.999902 -0.014032 0.000000 1.97431 MTRIX2 50 0.014032 0.999902 0.000000 -1.94680 MTRIX3 50 0.000000 0.000000 1.000000 -9.53340 MTRIX1 52 0.999975 -0.007016 0.000000 0.98374 MTRIX2 52 0.007016 0.999975 0.000000 -0.97686 MTRIX3 52 0.000000 0.000000 1.000000 -4.76670 MTRIX1 53 -0.999994 0.003508 0.000000 278.95003 MTRIX2 53 -0.003508 -0.999994 0.000000 279.93033 MTRIX3 53 0.000000 0.000000 1.000000 -2.38335 MTRIX1 55 -0.999994 -0.003508 0.000000 279.93033 MTRIX2 55 0.003508 -0.999994 0.000000 278.95003 MTRIX3 55 0.000000 0.000000 1.000000 2.38335 MTRIX1 56 0.999975 0.007016 0.000000 -0.97686 MTRIX2 56 -0.007016 0.999975 0.000000 0.98374 MTRIX3 56 0.000000 0.000000 1.000000 4.76670 TER 970 LEU A 129 CONECT 17 950 CONECT 207 858 CONECT 482 599 CONECT 570 693 CONECT 599 482 CONECT 693 570 CONECT 858 207 CONECT 950 17 MASTER 213 0 0 0 0 0 0 21 969 1 8 10 END