HEADER PROTEIN FIBRIL 27-OCT-22 8BG0 TITLE AMYLOID-BETA TETRAMERIC FILAMENTS WITH THE ARCTIC MUTATION (E22G) FROM TITLE 2 ALZHEIMER'S DISEASE BRAINS | ABETA40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: D, A, B, C; COMPND 4 SYNONYM: APP,ABPP,APPI,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 5 PRECURSOR PROTEIN,AMYLOID-BETA A4 PROTEIN,CEREBRAL VASCULAR AMYLOID COMPND 6 PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, AMYLOID-BETA, ARCTIC MUTATION, APP, FILAMENTS, E22G, E693G, KEYWDS 2 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 4 24-JUL-24 8BG0 1 REMARK REVDAT 3 22-FEB-23 8BG0 1 JRNL REVDAT 2 25-JAN-23 8BG0 1 JRNL REVDAT 1 18-JAN-23 8BG0 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. 1.99 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) : 1.990 REMARK 3 NUMBER OF PARTICLES : 115228 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 8BG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126277. 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 HUMAN BRAIN REMARK 245 WITH ARCTIC MUTATION (E693G) OF REMARK 245 ALZHEIMER'S DISEASE 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) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, A, B, C 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 350 BIOMT1 2 0.998671 -0.051546 0.000000 5.17917 REMARK 350 BIOMT2 2 0.051546 0.998671 0.000000 -4.91874 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -4.73584 REMARK 350 BIOMT1 3 0.998671 0.051546 0.000000 -4.91874 REMARK 350 BIOMT2 3 -0.051546 0.998671 0.000000 5.17917 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 4.73584 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 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 GLY D 38 REMARK 465 VAL D 39 REMARK 465 VAL D 40 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 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 GLY B 38 REMARK 465 VAL B 39 REMARK 465 VAL B 40 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 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 D 22 CB CG CD OE1 OE2 REMARK 470 GLU A 22 CB CG CD OE1 OE2 REMARK 470 GLU B 22 CB CG CD OE1 OE2 REMARK 470 GLU C 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 HIS D 14 72.23 62.57 REMARK 500 PHE D 20 78.40 73.24 REMARK 500 GLU D 22 -148.30 -94.26 REMARK 500 LYS A 16 56.25 38.40 REMARK 500 GLU A 22 -154.35 -95.54 REMARK 500 HIS B 14 72.43 62.48 REMARK 500 PHE B 20 77.99 73.36 REMARK 500 GLU B 22 -148.77 -94.95 REMARK 500 LYS C 16 55.90 38.16 REMARK 500 GLU C 22 -154.53 -95.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D 105 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH D 106 DISTANCE = 6.52 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-16023 RELATED DB: EMDB REMARK 900 AMYLOID-BETA TETRAMERIC FILAMENTS WITH THE ARCTIC MUTATION (E22G) REMARK 900 FROM ALZHEIMER'S DISEASE BRAINS | ABETA40 DBREF 8BG0 D 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 8BG0 A 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 8BG0 B 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 8BG0 C 1 40 UNP P05067 A4_HUMAN 616 655 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 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 FORMUL 5 HOH *12(H2 O) 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 0.978800 -0.204817 0.000000 22.13828 MTRIX2 2 0.204817 0.978800 0.000000 -17.98528 MTRIX3 2 0.000000 0.000000 1.000000 -18.94336 MTRIX1 3 0.988057 -0.154091 0.000000 16.26304 MTRIX2 3 0.154091 0.988057 0.000000 -13.92335 MTRIX3 3 0.000000 0.000000 1.000000 -14.20752 MTRIX1 4 0.994686 -0.102955 0.000000 10.60499 MTRIX2 4 0.102955 0.994686 0.000000 -9.56397 MTRIX3 4 0.000000 0.000000 1.000000 -9.47168 MTRIX1 5 0.998671 -0.051546 0.000000 5.17917 MTRIX2 5 0.051546 0.998671 0.000000 -4.91874 MTRIX3 5 0.000000 0.000000 1.000000 -4.73584 MTRIX1 6 0.998671 0.051546 0.000000 -4.91874 MTRIX2 6 -0.051546 0.998671 0.000000 5.17917 MTRIX3 6 0.000000 0.000000 1.000000 4.73584 MTRIX1 7 0.994686 0.102955 0.000000 -9.56397 MTRIX2 7 -0.102955 0.994686 0.000000 10.60499 MTRIX3 7 0.000000 0.000000 1.000000 9.47168 MTRIX1 8 0.988057 0.154091 0.000000 -13.92335 MTRIX2 8 -0.154091 0.988057 0.000000 16.26304 MTRIX3 8 0.000000 0.000000 1.000000 14.20752