HEADER PROTEIN FIBRIL 24-OCT-22 8BFB TITLE SARKOSYL-EXTRACTED APPNL-G-F ABETA42 FIBRIL STRUCTURE (METHOXY-X04- TITLE 2 LABELLED MICE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 SYNONYM: APP,ABPP,APPI,ALZHEIMER DISEASE AMYLOID A4 PROTEIN HOMOLOG, COMPND 5 ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID PRECURSOR PROTEIN,AMYLOID- COMPND 6 BETA (A4) PRECURSOR PROTEIN,AMYLOID-BETA A4 PROTEIN,CEREBRAL VASCULAR COMPND 7 AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II; COMPND 8 OTHER_DETAILS: HUMANISED ABETA42 FROM APP^NL-G-F MICE WITH ARCTIC COMPND 9 MUTATION (E22G) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 TISSUE: BRAIN KEYWDS AMYLOID, FIBRIL, HELICAL, CROSS-BETA, BETA AMYLOID, PROTEIN FIBRIL, KEYWDS 2 EX VIVO, ARCTIC MUTANT, ALZHEIMERS DISEASE EXPDTA ELECTRON MICROSCOPY AUTHOR M.WILKINSON,C.LEISTNER,A.BURGESS,S.GOODFELLOW,S.DEUCHARS,N.A.RANSON, AUTHOR 2 S.E.RADFORD,R.A.W.FRANK REVDAT 2 24-JUL-24 8BFB 1 REMARK REVDAT 1 31-MAY-23 8BFB 0 JRNL AUTH C.LEISTNER,M.WILKINSON,A.BURGESS,M.LOVATT,S.GOODBODY,Y.XU, JRNL AUTH 2 S.DEUCHARS,S.E.RADFORD,N.A.RANSON,R.A.W.FRANK JRNL TITL THE IN-TISSUE MOLECULAR ARCHITECTURE OF BETA-AMYLOID JRNL TITL 2 PATHOLOGY IN THE MAMMALIAN BRAIN. JRNL REF NAT COMMUN V. 14 2833 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37198197 JRNL DOI 10.1038/S41467-023-38495-5 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, CTFFIND, COOT, RELION, REMARK 3 RELION, RELION, RELION, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 52.000 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 3640 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 8BFB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292125276. 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 : SARKOSYL-EXTRACTED APPNL-G-F REMARK 245 ABETA42 FIBRIL REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 6S BLOT REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : FIBRILS PURIFIED FROM MOUSE REMARK 245 BRAIN LABELLED WITH METHOXY-X04 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4165 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) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2900.00 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) : 4100.00 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: 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 VAL A 39 REMARK 465 VAL A 40 REMARK 465 ILE A 41 REMARK 465 ALA A 42 REMARK 465 VAL B 39 REMARK 465 VAL B 40 REMARK 465 ILE B 41 REMARK 465 ALA B 42 REMARK 465 VAL C 39 REMARK 465 VAL C 40 REMARK 465 ILE C 41 REMARK 465 ALA C 42 REMARK 465 VAL D 39 REMARK 465 VAL D 40 REMARK 465 ILE D 41 REMARK 465 ALA D 42 REMARK 465 VAL E 39 REMARK 465 VAL E 40 REMARK 465 ILE E 41 REMARK 465 ALA E 42 REMARK 465 VAL F 39 REMARK 465 VAL F 40 REMARK 465 ILE F 41 REMARK 465 ALA F 42 REMARK 465 VAL G 39 REMARK 465 VAL G 40 REMARK 465 ILE G 41 REMARK 465 ALA G 42 REMARK 465 VAL H 39 REMARK 465 VAL H 40 REMARK 465 ILE H 41 REMARK 465 ALA H 42 REMARK 465 VAL I 39 REMARK 465 VAL I 40 REMARK 465 ILE I 41 REMARK 465 ALA I 42 REMARK 465 VAL J 39 REMARK 465 VAL J 40 REMARK 465 ILE J 41 REMARK 465 ALA J 42 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16019 RELATED DB: EMDB REMARK 900 SARKOSYL-EXTRACTED APPNL-G-F ABETA42 FIBRIL STRUCTURE (METHOXY-X04- REMARK 900 LABELLED MICE) DBREF 8BFB A 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB B 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB C 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB D 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB E 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB F 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB G 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB H 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB I 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 8BFB J 1 42 UNP P05067 A4_HUMAN 672 713 SEQADV 8BFB GLY A 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY B 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY C 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY D 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY E 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY F 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY G 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY H 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY I 22 UNP P05067 GLU 693 VARIANT SEQADV 8BFB GLY J 22 UNP P05067 GLU 693 VARIANT SEQRES 1 A 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 A 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 42 VAL ILE ALA SEQRES 1 B 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 B 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 B 42 VAL ILE ALA SEQRES 1 C 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 C 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 42 VAL ILE ALA SEQRES 1 D 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 D 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 D 42 VAL ILE ALA SEQRES 1 E 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 E 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 E 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 E 42 VAL ILE ALA SEQRES 1 F 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 F 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 F 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 F 42 VAL ILE ALA SEQRES 1 G 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 G 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 G 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 G 42 VAL ILE ALA SEQRES 1 H 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 H 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 H 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 H 42 VAL ILE ALA SEQRES 1 I 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 I 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 I 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 I 42 VAL ILE ALA SEQRES 1 J 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 J 42 HIS GLN LYS LEU VAL PHE PHE ALA GLY ASP VAL GLY SER SEQRES 3 J 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 J 42 VAL ILE ALA SHEET 1 AA1 5 GLU A 3 ASP A 7 0 SHEET 2 AA1 5 GLU C 3 ASP C 7 1 O GLU C 3 N PHE A 4 SHEET 3 AA1 5 GLU E 3 ASP E 7 1 O GLU E 3 N PHE C 4 SHEET 4 AA1 5 GLU G 3 ASP G 7 1 O GLU G 3 N PHE E 4 SHEET 5 AA1 5 GLU I 3 ASP I 7 1 O GLU I 3 N PHE G 4 SHEET 1 AA2 5 TYR A 10 LYS A 16 0 SHEET 2 AA2 5 TYR C 10 LYS C 16 1 O TYR C 10 N GLU A 11 SHEET 3 AA2 5 TYR E 10 LYS E 16 1 O HIS E 14 N HIS C 13 SHEET 4 AA2 5 TYR G 10 LYS G 16 1 O HIS G 14 N HIS E 13 SHEET 5 AA2 5 TYR I 10 LYS I 16 1 O HIS I 14 N HIS G 13 SHEET 1 AA3 5 PHE A 20 ALA A 21 0 SHEET 2 AA3 5 PHE C 20 ALA C 21 1 O PHE C 20 N ALA A 21 SHEET 3 AA3 5 PHE E 20 ALA E 21 1 O PHE E 20 N ALA C 21 SHEET 4 AA3 5 PHE G 20 ALA G 21 1 O PHE G 20 N ALA E 21 SHEET 5 AA3 5 PHE I 20 ALA I 21 1 O PHE I 20 N ALA G 21 SHEET 1 AA4 5 VAL A 24 ASN A 27 0 SHEET 2 AA4 5 VAL C 24 ASN C 27 1 O VAL C 24 N GLY A 25 SHEET 3 AA4 5 VAL E 24 ASN E 27 1 O VAL E 24 N GLY C 25 SHEET 4 AA4 5 VAL G 24 ASN G 27 1 O VAL G 24 N GLY E 25 SHEET 5 AA4 5 VAL I 24 ASN I 27 1 O VAL I 24 N GLY G 25 SHEET 1 AA5 5 ALA A 30 VAL A 36 0 SHEET 2 AA5 5 ALA C 30 VAL C 36 1 O ILE C 31 N ALA A 30 SHEET 3 AA5 5 ALA E 30 VAL E 36 1 O ILE E 31 N ALA C 30 SHEET 4 AA5 5 ALA G 30 VAL G 36 1 O ILE G 31 N ALA E 30 SHEET 5 AA5 5 ALA I 30 VAL I 36 1 O ILE I 31 N ALA G 30 SHEET 1 AA6 5 GLU B 3 ASP B 7 0 SHEET 2 AA6 5 GLU D 3 ASP D 7 1 O GLU D 3 N PHE B 4 SHEET 3 AA6 5 GLU F 3 ASP F 7 1 O GLU F 3 N PHE D 4 SHEET 4 AA6 5 GLU H 3 ASP H 7 1 O GLU H 3 N PHE F 4 SHEET 5 AA6 5 GLU J 3 ASP J 7 1 O GLU J 3 N PHE H 4 SHEET 1 AA7 5 TYR B 10 LYS B 16 0 SHEET 2 AA7 5 TYR D 10 LYS D 16 1 O HIS D 14 N HIS B 13 SHEET 3 AA7 5 TYR F 10 LYS F 16 1 O HIS F 14 N HIS D 13 SHEET 4 AA7 5 TYR H 10 LYS H 16 1 O HIS H 14 N HIS F 13 SHEET 5 AA7 5 TYR J 10 LYS J 16 1 O TYR J 10 N GLU H 11 SHEET 1 AA8 5 PHE B 20 ALA B 21 0 SHEET 2 AA8 5 PHE D 20 ALA D 21 1 O PHE D 20 N ALA B 21 SHEET 3 AA8 5 PHE F 20 ALA F 21 1 O PHE F 20 N ALA D 21 SHEET 4 AA8 5 PHE H 20 ALA H 21 1 O PHE H 20 N ALA F 21 SHEET 5 AA8 5 PHE J 20 ALA J 21 1 O PHE J 20 N ALA H 21 SHEET 1 AA9 5 VAL B 24 ASN B 27 0 SHEET 2 AA9 5 VAL D 24 ASN D 27 1 O VAL D 24 N GLY B 25 SHEET 3 AA9 5 VAL F 24 ASN F 27 1 O VAL F 24 N GLY D 25 SHEET 4 AA9 5 VAL H 24 ASN H 27 1 O VAL H 24 N GLY F 25 SHEET 5 AA9 5 VAL J 24 ASN J 27 1 O VAL J 24 N GLY H 25 SHEET 1 AB1 5 ALA B 30 VAL B 36 0 SHEET 2 AB1 5 ALA D 30 VAL D 36 1 O ILE D 31 N ALA B 30 SHEET 3 AB1 5 ALA F 30 VAL F 36 1 O ILE F 31 N ALA D 30 SHEET 4 AB1 5 ALA H 30 VAL H 36 1 O ILE H 31 N ALA F 30 SHEET 5 AB1 5 ALA J 30 VAL J 36 1 O ILE J 31 N ALA H 30 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