HEADER PROTEIN FIBRIL 26-APR-23 8OVK TITLE LIPIDIC AMYLOID-BETA(1-40) FIBRIL - POLYMORPH L1 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 8OVK 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. 2.88 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) : 2.880 REMARK 3 NUMBER OF PARTICLES : 177981 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 8OVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292130110. 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 L1 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 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 GLU A 3 -64.36 -126.49 REMARK 500 GLU B 3 -64.37 -126.52 REMARK 500 GLU C 3 -64.36 -126.50 REMARK 500 GLU D 3 -64.33 -126.53 REMARK 500 GLU E 3 -64.40 -126.48 REMARK 500 GLU F 3 -64.36 -126.51 REMARK 500 GLU G 3 -64.41 -126.54 REMARK 500 GLU H 3 -64.38 -126.51 REMARK 500 GLU I 3 -64.39 -126.52 REMARK 500 GLU J 3 -64.35 -126.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17218 RELATED DB: EMDB REMARK 900 LIPIDIC AMYLOID-BETA(1-40) FIBRIL - POLYMORPH L1 REMARK 900 RELATED ID: EMD-17223 RELATED DB: EMDB REMARK 900 RELATED ID: 8OVM RELATED DB: PDB REMARK 900 RELATED ID: EMD-17234 RELATED DB: EMDB REMARK 900 RELATED ID: 8OWD RELATED DB: PDB REMARK 900 RELATED ID: EMD-17235 RELATED DB: EMDB REMARK 900 RELATED ID: 8OWE RELATED DB: PDB REMARK 900 RELATED ID: EMD-17238 RELATED DB: EMDB REMARK 900 RELATED ID: 8OWJ RELATED DB: PDB REMARK 900 RELATED ID: EMD-17239 RELATED DB: EMDB REMARK 900 RELATED ID: 8OWK RELATED DB: PDB DBREF 8OVK A 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK B 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK C 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK D 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK E 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK F 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK G 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK H 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK I 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OVK 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 HIS A 13 0 SHEET 2 AA1 5 TYR C 10 HIS C 13 1 O VAL C 12 N HIS A 13 SHEET 3 AA1 5 TYR E 10 HIS E 13 1 O VAL E 12 N HIS C 13 SHEET 4 AA1 5 TYR G 10 HIS G 13 1 O VAL G 12 N HIS E 13 SHEET 5 AA1 5 TYR I 10 HIS I 13 1 O VAL I 12 N HIS G 13 SHEET 1 AA2 5 LYS A 16 VAL A 24 0 SHEET 2 AA2 5 LYS C 16 VAL C 24 1 O PHE C 19 N VAL A 18 SHEET 3 AA2 5 LYS E 16 VAL E 24 1 O PHE E 19 N VAL C 18 SHEET 4 AA2 5 LYS G 16 VAL G 24 1 O PHE G 19 N VAL E 18 SHEET 5 AA2 5 LYS I 16 VAL I 24 1 O PHE I 19 N VAL G 18 SHEET 1 AA3 5 ILE A 31 VAL A 39 0 SHEET 2 AA3 5 ILE C 31 VAL C 39 1 O VAL C 36 N GLY A 37 SHEET 3 AA3 5 ILE E 31 VAL E 39 1 O VAL E 36 N GLY C 37 SHEET 4 AA3 5 ILE G 31 VAL G 39 1 O VAL G 36 N GLY E 37 SHEET 5 AA3 5 ILE I 31 VAL I 39 1 O VAL I 36 N GLY G 37 SHEET 1 AA4 5 TYR B 10 HIS B 13 0 SHEET 2 AA4 5 TYR D 10 HIS D 13 1 O VAL D 12 N HIS B 13 SHEET 3 AA4 5 TYR F 10 HIS F 13 1 O VAL F 12 N HIS D 13 SHEET 4 AA4 5 TYR H 10 HIS H 13 1 O VAL H 12 N HIS F 13 SHEET 5 AA4 5 TYR J 10 HIS J 13 1 O VAL J 12 N HIS H 13 SHEET 1 AA5 5 LYS B 16 VAL B 24 0 SHEET 2 AA5 5 LYS D 16 VAL D 24 1 O PHE D 19 N VAL B 18 SHEET 3 AA5 5 LYS F 16 VAL F 24 1 O PHE F 19 N VAL D 18 SHEET 4 AA5 5 LYS H 16 VAL H 24 1 O PHE H 19 N VAL F 18 SHEET 5 AA5 5 LYS J 16 VAL J 24 1 O PHE J 19 N VAL H 18 SHEET 1 AA6 5 ILE B 31 VAL B 39 0 SHEET 2 AA6 5 ILE D 31 VAL D 39 1 O VAL D 36 N GLY B 37 SHEET 3 AA6 5 ILE F 31 VAL F 39 1 O VAL F 36 N GLY D 37 SHEET 4 AA6 5 ILE H 31 VAL H 39 1 O VAL H 36 N GLY F 37 SHEET 5 AA6 5 ILE J 31 VAL J 39 1 O VAL J 36 N GLY H 37 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 -0.999980 -0.006384 -0.000002 263.33530 1 MTRIX2 1 0.006384 -0.999980 0.000001 261.65943 1 MTRIX3 1 -0.000002 0.000001 1.000000 2.35407 1 MTRIX1 2 0.999918 0.012770 0.000000 -1.66539 1 MTRIX2 2 -0.012770 0.999918 0.000000 1.68674 1 MTRIX3 2 0.000000 0.000000 1.000000 4.70802 1 MTRIX1 3 -0.999817 -0.019155 0.000001 264.99002 1 MTRIX2 3 0.019155 -0.999817 0.000000 259.96182 1 MTRIX3 3 0.000001 0.000000 1.000000 7.06197 1 MTRIX1 4 0.999674 0.025538 0.000001 -3.30914 1 MTRIX2 4 -0.025538 0.999674 0.000000 3.39473 1 MTRIX3 4 -0.000001 0.000000 1.000000 9.41603 1 MTRIX1 5 -0.999490 -0.031920 0.000000 266.62267 1 MTRIX2 5 0.031920 -0.999490 0.000000 258.24359 1 MTRIX3 5 0.000000 0.000000 1.000000 11.77000 1 MTRIX1 6 0.999266 0.038302 0.000000 -4.93079 1 MTRIX2 6 -0.038302 0.999266 0.000000 5.12340 1 MTRIX3 6 0.000000 0.000000 1.000000 14.12398 1 MTRIX1 7 -0.999001 -0.044681 0.000000 268.23323 1 MTRIX2 7 0.044681 -0.999001 0.000000 256.50464 1 MTRIX3 7 0.000000 0.000000 1.000000 16.47799 1 MTRIX1 8 0.998696 0.051060 0.000001 -6.53039 1 MTRIX2 8 -0.051060 0.998696 0.000000 6.87278 1 MTRIX3 8 -0.000001 0.000000 1.000000 18.83202 1 MTRIX1 9 -0.998349 -0.057435 0.000001 269.82162 1 MTRIX2 9 0.057435 -0.998349 -0.000001 254.74505 1 MTRIX3 9 0.000001 -0.000001 1.000000 21.18595 1