HEADER PROTEIN FIBRIL 27-OCT-22 8BG9 TITLE MURINE AMYLOID-BETA FILAMENTS WITH THE ARCTIC MUTATION (E22G) FROM TITLE 2 APP(NL-G-F) MOUSE BRAINS | ABETA COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PROTEIN 40; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ABETA40,BETA-APP40 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090 KEYWDS AMYLOID, AMYLOID-BETA, ARCTIC MUTATION, APP, NL-G-F, MOUSE BRAINS, KEYWDS 2 FILAMENTS, E22G, E693G, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.YANG,W.J.ZHANG,A.G.MURZIN,M.SCHWEIGHAUSER,M.HUANG,S.K.A.LOVESTAM, AUTHOR 2 S.Y.PEAK-CHEW,J.MACDONALD,I.LAVENIR,B.GHETTI,C.GRAFF,A.KUMAR, AUTHOR 3 A.NORDBER,M.GOEDERT,S.H.W.SCHERES REVDAT 3 22-FEB-23 8BG9 1 JRNL REVDAT 2 25-JAN-23 8BG9 1 JRNL REVDAT 1 18-JAN-23 8BG9 0 JRNL AUTH Y.YANG,W.ZHANG,A.G.MURZIN,M.SCHWEIGHAUSER,M.HUANG, JRNL AUTH 2 S.LOVESTAM,S.Y.PEAK-CHEW,T.SAITO,T.C.SAIDO,J.MACDONALD, JRNL AUTH 3 I.LAVENIR,B.GHETTI,C.GRAFF,A.KUMAR,A.NORDBERG,M.GOEDERT, JRNL AUTH 4 S.H.W.SCHERES JRNL TITL CRYO-EM STRUCTURES OF AMYLOID-BETA FILAMENTS WITH THE ARCTIC JRNL TITL 2 MUTATION (E22G) FROM HUMAN AND MOUSE BRAINS. JRNL REF ACTA NEUROPATHOL V. 145 325 2023 JRNL REFN ESSN 1432-0533 JRNL PMID 36611124 JRNL DOI 10.1007/S00401-022-02533-1 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, COOT, REFMAC, REMARK 3 RELION, RELION, RELION, 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 : 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 39823 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 8BG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126279. 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 : AMYLOID-BETA FILAMENTS REMARK 245 EXTRACTED FROM THE MOUSE BRAINS REMARK 245 WITH APP NL-G-F MUTATIONS 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 : 7.50 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) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2600.00 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 0.999740 0.022792 0.000000 -2.71288 REMARK 350 BIOMT2 1 -0.022792 0.999740 0.000000 2.77544 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -4.92018 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 0.999740 -0.022792 0.000000 2.77544 REMARK 350 BIOMT2 3 0.022792 0.999740 0.000000 -2.71288 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 4.92018 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 22 CB CG CD OE1 OE2 REMARK 470 GLU B 22 CB CG CD OE1 OE2 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 LYS A 16 135.73 -170.27 REMARK 500 GLU A 22 -165.88 140.51 REMARK 500 LEU A 34 123.31 -178.05 REMARK 500 VAL B 12 140.24 -170.34 REMARK 500 GLU B 22 -163.14 139.21 REMARK 500 VAL B 24 -50.03 -124.10 REMARK 500 ALA B 30 96.84 -161.75 REMARK 500 LEU B 34 123.09 -178.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16027 RELATED DB: EMDB REMARK 900 MURINE AMYLOID-BETA FILAMENTS WITH THE ARCTIC MUTATION (E22G) FROM REMARK 900 APP(NL-G-F) MOUSE BRAINS | ABETA DBREF 8BG9 A 1 37 UNP P12023 A4_MOUSE 672 708 DBREF 8BG9 B 1 37 UNP P12023 A4_MOUSE 672 708 SEQADV 8BG9 ARG A 5 UNP P12023 GLY 676 CONFLICT SEQADV 8BG9 TYR A 10 UNP P12023 PHE 681 CONFLICT SEQADV 8BG9 HIS A 13 UNP P12023 ARG 684 CONFLICT SEQADV 8BG9 ARG B 5 UNP P12023 GLY 676 CONFLICT SEQADV 8BG9 TYR B 10 UNP P12023 PHE 681 CONFLICT SEQADV 8BG9 HIS B 13 UNP P12023 ARG 684 CONFLICT SEQRES 1 A 37 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 37 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 37 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY SEQRES 1 B 37 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 37 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 B 37 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY 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 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.999740 -0.022792 0.000000 2.77544 MTRIX2 2 0.022792 0.999740 0.000000 -2.71288 MTRIX3 2 0.000000 0.000000 1.000000 4.92018 MTRIX1 3 0.999740 0.022792 0.000000 -2.71288 MTRIX2 3 -0.022792 0.999740 0.000000 2.77544 MTRIX3 3 0.000000 0.000000 1.000000 -4.92018