HEADER PROTEIN FIBRIL 27-APR-23 8OWE TITLE LIPIDIC AMYLOID-BETA(1-40) FIBRIL - POLYMORPH L2-L3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA A4 PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS AMYLOID-BETA, FIBRIL, LIPIDS, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR B.FRIEG,M.HAN,K.GILLER,C.DIENEMANN,D.RIEDEL,S.BECKER,L.B.ANDREAS, AUTHOR 2 C.GRIESINGER,G.F.SCHROEDER REVDAT 1 06-MAR-24 8OWE 0 JRNL AUTH B.FRIEG,M.HAN,K.GILLER,C.DIENEMANN,D.RIEDEL,S.BECKER, JRNL AUTH 2 L.B.ANDREAS,C.GRIESINGER,G.F.SCHRODER JRNL TITL CRYO-EM STRUCTURES OF LIPIDIC FIBRILS OF AMYLOID-BETA JRNL TITL 2 (1-40). JRNL REF NAT COMMUN V. 15 1297 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38351005 JRNL DOI 10.1038/S41467-023-43822-X REMARK 2 REMARK 2 RESOLUTION. 3.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 3.750 REMARK 3 NUMBER OF PARTICLES : 13034 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8OWE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292130172. 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 : THE L2-L3 AMYLOID-BETA(1-40) REMARK 245 FIBRIL IN COMPLEX WITH LIPIDS 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 : 6.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 4000.00 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 ASP A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 ASP B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 ASP C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 ASP D 1 REMARK 465 ALA D 2 REMARK 465 GLU D 3 REMARK 465 ASP E 1 REMARK 465 ALA E 2 REMARK 465 GLU E 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP B 7 NE ARG C 5 1.83 REMARK 500 OD2 ASP C 7 NE ARG D 5 1.83 REMARK 500 OD2 ASP A 7 NE ARG B 5 1.83 REMARK 500 OD2 ASP D 7 NE ARG E 5 1.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG F 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG G 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG H 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG I 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG J 5 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES 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 5 0.08 SIDE CHAIN REMARK 500 ARG B 5 0.08 SIDE CHAIN REMARK 500 ARG C 5 0.08 SIDE CHAIN REMARK 500 ARG D 5 0.08 SIDE CHAIN REMARK 500 ARG E 5 0.08 SIDE CHAIN REMARK 500 ASP F 1 0.09 SIDE CHAIN REMARK 500 HIS F 13 0.09 SIDE CHAIN REMARK 500 ASP G 1 0.09 SIDE CHAIN REMARK 500 HIS G 13 0.09 SIDE CHAIN REMARK 500 ASP H 1 0.09 SIDE CHAIN REMARK 500 HIS H 13 0.09 SIDE CHAIN REMARK 500 ASP I 1 0.09 SIDE CHAIN REMARK 500 HIS I 13 0.09 SIDE CHAIN REMARK 500 ASP J 1 0.09 SIDE CHAIN REMARK 500 HIS J 13 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8OVK RELATED DB: PDB REMARK 900 RELATED ID: EMD-17218 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-17235 RELATED DB: EMDB REMARK 900 LIPIDIC AMYLOID-BETA(1-40) FIBRIL - POLYMORPH L2-L3 DBREF 8OWE A 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE B 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE C 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE D 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE E 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE F 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE G 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE H 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE I 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OWE J 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 SEQRES 1 A 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 40 VAL SEQRES 1 B 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 B 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 B 40 VAL SEQRES 1 C 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 40 VAL SEQRES 1 D 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 D 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 D 40 VAL SEQRES 1 E 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 E 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 E 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 E 40 VAL SEQRES 1 F 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 F 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 F 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 F 40 VAL SEQRES 1 G 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 G 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 G 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 G 40 VAL SEQRES 1 H 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 H 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 H 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 H 40 VAL SEQRES 1 I 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 I 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 I 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 I 40 VAL SEQRES 1 J 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 J 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 J 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 J 40 VAL SHEET 1 AA1 5 TYR A 10 GLU A 11 0 SHEET 2 AA1 5 TYR B 10 GLU B 11 1 O GLU B 11 N TYR A 10 SHEET 3 AA1 5 TYR C 10 GLU C 11 1 O GLU C 11 N TYR B 10 SHEET 4 AA1 5 TYR D 10 GLU D 11 1 O GLU D 11 N TYR C 10 SHEET 5 AA1 5 TYR E 10 GLU E 11 1 O GLU E 11 N TYR D 10 SHEET 1 AA2 5 LYS A 16 ASP A 23 0 SHEET 2 AA2 5 LYS B 16 ASP B 23 1 O PHE B 20 N ALA A 21 SHEET 3 AA2 5 LYS C 16 ASP C 23 1 O PHE C 20 N ALA B 21 SHEET 4 AA2 5 LYS D 16 ASP D 23 1 O PHE D 20 N ALA C 21 SHEET 5 AA2 5 LYS E 16 ASP E 23 1 O PHE E 20 N ALA D 21 SHEET 1 AA3 5 ALA F 2 ASP F 23 0 SHEET 2 AA3 5 ALA G 2 ASP G 23 1 O HIS G 13 N VAL F 12 SHEET 3 AA3 5 ALA H 2 ASP H 23 1 O HIS H 13 N VAL G 12 SHEET 4 AA3 5 ALA I 2 ASP I 23 1 O HIS I 13 N VAL H 12 SHEET 5 AA3 5 ALA J 2 ASP J 23 1 O HIS J 13 N VAL I 12 SHEET 1 AA4 5 GLY F 29 VAL F 36 0 SHEET 2 AA4 5 GLY G 29 VAL G 36 1 O LEU G 34 N MET F 35 SHEET 3 AA4 5 GLY H 29 VAL H 36 1 O LEU H 34 N MET G 35 SHEET 4 AA4 5 GLY I 29 VAL I 36 1 O LEU I 34 N MET H 35 SHEET 5 AA4 5 GLY J 29 VAL J 36 1 O LEU J 34 N MET I 35 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 1 0.999568 0.029401 0.000000 -3.80212 1 MTRIX2 1 -0.029401 0.999568 0.000001 3.91544 1 MTRIX3 1 0.000000 -0.000001 1.000000 4.65016 1 MTRIX1 2 0.998271 0.058774 0.000000 -7.48717 1 MTRIX2 2 -0.058774 0.998271 0.000000 7.94098 1 MTRIX3 2 0.000000 0.000000 1.000000 9.30001 1 MTRIX1 3 0.996112 0.088096 0.000000 -11.05233 1 MTRIX2 3 -0.088096 0.996112 0.000000 12.07292 1 MTRIX3 3 0.000000 0.000000 1.000000 13.95001 1 MTRIX1 4 0.993091 0.117345 -0.000001 -14.49459 1 MTRIX2 4 -0.117345 0.993091 0.000000 16.30827 1 MTRIX3 4 0.000001 0.000000 1.000000 18.59990 1 MTRIX1 5 0.455153 0.878631 0.144372 -23.47917 1 MTRIX2 5 -0.825988 0.477187 -0.300061 254.13955 1 MTRIX3 5 -0.332535 0.017324 0.942932 49.02102 1 MTRIX1 6 0.430673 0.892280 0.135489 -19.79951 1 MTRIX2 6 -0.839012 0.451150 -0.304175 258.63533 1 MTRIX3 6 -0.332535 0.017323 0.942932 53.67105 1 MTRIX1 7 0.405821 0.905157 0.126489 -15.98939 1 MTRIX2 7 -0.851311 0.424723 -0.308027 263.02077 1 MTRIX3 7 -0.332535 0.017322 0.942932 58.32119 1 MTRIX1 8 0.380617 0.917253 0.117377 -12.05155 1 MTRIX2 8 -0.862874 0.397928 -0.311612 267.29271 1 MTRIX3 8 -0.332535 0.017324 0.942932 62.97100 1 MTRIX1 9 0.355086 0.928555 0.108169 -7.99065 1 MTRIX2 9 -0.873690 0.370791 -0.314928 271.44649 1 MTRIX3 9 -0.332536 0.017320 0.942932 67.62148 1