HEADER PROTEIN FIBRIL 20-APR-23 8OT1 TITLE UNSEEDED ABETA(1-40) AMYLOID FIBRIL (MORPHOLOGY I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA A4 PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L; 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: RV308 KEYWDS AMYLOID FIBRIL, AMYLOID-BETA, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR P.B.PFEIFFER,M.SCHMIDT,M.FAENDRICH REVDAT 1 07-FEB-24 8OT1 0 JRNL AUTH P.B.PFEIFFER,M.UGRINA,N.SCHWIERZ,C.J.SIGURDSON,M.SCHMIDT, JRNL AUTH 2 M.FANDRICH JRNL TITL CRYO-EM ANALYSIS OF THE EFFECT OF SEEDING WITH BRAIN-DERIVED JRNL TITL 2 A BETA AMYLOID FIBRILS. JRNL REF J.MOL.BIOL. V. 436 68422 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 38158175 JRNL DOI 10.1016/J.JMB.2023.168422 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, CTFFIND, COOT, REMARK 3 PHENIX, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : BACKBONE TRACE REMARK 3 REFINEMENT TARGET : CORRLEATION COEFFICIENT 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) : 2.590 REMARK 3 NUMBER OF PARTICLES : 176139 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 8OT1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129974. 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 : IN VITRO ABETA(1-40) AMYLOID REMARK 245 FIBRIL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.01 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : MORPHOLOGY I REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4628 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2100.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 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 : 130000 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 30880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -194.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L 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 PHE A 4 REMARK 465 ARG A 5 REMARK 465 HIS A 6 REMARK 465 ASP A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 TYR A 10 REMARK 465 GLU A 11 REMARK 465 VAL A 12 REMARK 465 ASP B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 PHE B 4 REMARK 465 ARG B 5 REMARK 465 HIS B 6 REMARK 465 ASP B 7 REMARK 465 SER B 8 REMARK 465 GLY B 9 REMARK 465 TYR B 10 REMARK 465 GLU B 11 REMARK 465 VAL B 12 REMARK 465 ASP C 1 REMARK 465 ALA C 2 REMARK 465 GLU C 3 REMARK 465 PHE C 4 REMARK 465 ARG C 5 REMARK 465 HIS C 6 REMARK 465 ASP C 7 REMARK 465 SER C 8 REMARK 465 GLY C 9 REMARK 465 TYR C 10 REMARK 465 GLU C 11 REMARK 465 VAL C 12 REMARK 465 ASP D 1 REMARK 465 ALA D 2 REMARK 465 GLU D 3 REMARK 465 PHE D 4 REMARK 465 ARG D 5 REMARK 465 HIS D 6 REMARK 465 ASP D 7 REMARK 465 SER D 8 REMARK 465 GLY D 9 REMARK 465 TYR D 10 REMARK 465 GLU D 11 REMARK 465 VAL D 12 REMARK 465 ASP E 1 REMARK 465 ALA E 2 REMARK 465 GLU E 3 REMARK 465 PHE E 4 REMARK 465 ARG E 5 REMARK 465 HIS E 6 REMARK 465 ASP E 7 REMARK 465 SER E 8 REMARK 465 GLY E 9 REMARK 465 TYR E 10 REMARK 465 GLU E 11 REMARK 465 VAL E 12 REMARK 465 ASP F 1 REMARK 465 ALA F 2 REMARK 465 GLU F 3 REMARK 465 PHE F 4 REMARK 465 ARG F 5 REMARK 465 HIS F 6 REMARK 465 ASP F 7 REMARK 465 SER F 8 REMARK 465 GLY F 9 REMARK 465 TYR F 10 REMARK 465 GLU F 11 REMARK 465 VAL F 12 REMARK 465 ASP G 1 REMARK 465 ALA G 2 REMARK 465 GLU G 3 REMARK 465 PHE G 4 REMARK 465 ARG G 5 REMARK 465 HIS G 6 REMARK 465 ASP G 7 REMARK 465 SER G 8 REMARK 465 GLY G 9 REMARK 465 TYR G 10 REMARK 465 GLU G 11 REMARK 465 VAL G 12 REMARK 465 ASP H 1 REMARK 465 ALA H 2 REMARK 465 GLU H 3 REMARK 465 PHE H 4 REMARK 465 ARG H 5 REMARK 465 HIS H 6 REMARK 465 ASP H 7 REMARK 465 SER H 8 REMARK 465 GLY H 9 REMARK 465 TYR H 10 REMARK 465 GLU H 11 REMARK 465 VAL H 12 REMARK 465 ASP I 1 REMARK 465 ALA I 2 REMARK 465 GLU I 3 REMARK 465 PHE I 4 REMARK 465 ARG I 5 REMARK 465 HIS I 6 REMARK 465 ASP I 7 REMARK 465 SER I 8 REMARK 465 GLY I 9 REMARK 465 TYR I 10 REMARK 465 GLU I 11 REMARK 465 VAL I 12 REMARK 465 ASP J 1 REMARK 465 ALA J 2 REMARK 465 GLU J 3 REMARK 465 PHE J 4 REMARK 465 ARG J 5 REMARK 465 HIS J 6 REMARK 465 ASP J 7 REMARK 465 SER J 8 REMARK 465 GLY J 9 REMARK 465 TYR J 10 REMARK 465 GLU J 11 REMARK 465 VAL J 12 REMARK 465 ASP K 1 REMARK 465 ALA K 2 REMARK 465 GLU K 3 REMARK 465 PHE K 4 REMARK 465 ARG K 5 REMARK 465 HIS K 6 REMARK 465 ASP K 7 REMARK 465 SER K 8 REMARK 465 GLY K 9 REMARK 465 TYR K 10 REMARK 465 GLU K 11 REMARK 465 VAL K 12 REMARK 465 ASP L 1 REMARK 465 ALA L 2 REMARK 465 GLU L 3 REMARK 465 PHE L 4 REMARK 465 ARG L 5 REMARK 465 HIS L 6 REMARK 465 ASP L 7 REMARK 465 SER L 8 REMARK 465 GLY L 9 REMARK 465 TYR L 10 REMARK 465 GLU L 11 REMARK 465 VAL L 12 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17166 RELATED DB: EMDB REMARK 900 UNSEEDED ABETA(1-40) AMYLOID FIBRIL (MORPHOLOGY I) DBREF 8OT1 A 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 B 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 C 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 D 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 E 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 F 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 G 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 H 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 I 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 J 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 K 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8OT1 L 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 SEQRES 1 K 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 K 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 K 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 K 40 VAL SEQRES 1 L 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 L 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 L 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 L 40 VAL SHEET 1 AA1 6 LYS A 16 VAL A 24 0 SHEET 2 AA1 6 LYS C 16 VAL C 24 1 O PHE C 19 N VAL A 18 SHEET 3 AA1 6 LYS E 16 VAL E 24 1 O PHE E 19 N VAL C 18 SHEET 4 AA1 6 LYS G 16 VAL G 24 1 O PHE G 19 N VAL E 18 SHEET 5 AA1 6 LYS I 16 VAL I 24 1 O PHE I 19 N VAL G 18 SHEET 6 AA1 6 LYS K 16 VAL K 24 1 O PHE K 19 N VAL I 18 SHEET 1 AA2 6 LYS B 16 VAL B 24 0 SHEET 2 AA2 6 LYS D 16 VAL D 24 1 O PHE D 19 N VAL B 18 SHEET 3 AA2 6 LYS F 16 VAL F 24 1 O PHE F 19 N VAL D 18 SHEET 4 AA2 6 LYS H 16 VAL H 24 1 O PHE H 19 N VAL F 18 SHEET 5 AA2 6 LYS J 16 VAL J 24 1 O PHE J 19 N VAL H 18 SHEET 6 AA2 6 LYS L 16 VAL L 24 1 O PHE L 19 N VAL J 18 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