HEADER PROTEIN FIBRIL 06-SEP-22 8AZS TITLE TYPE I AMYLOID-BETA 42 FILAMENTS FROM HIGH-SPIN SUPERNATANTS OF TITLE 2 AQUEOUS EXTRACTS FROM ALZHEIMER'S DISEASE BRAINS | ABETA42 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: H; 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, FILAMENTS, ABETA42, AMYLOID-BETA, CRYO-EM, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.YANG,M.A.STERN,L.A.MEUNIER,W.LIU,Y.Q.CAI,M.ERICSSON,L.LIU, AUTHOR 2 J.D.SELKOE,M.GOEDERT,H.W.S.SCHERES REVDAT 4 24-JUL-24 8AZS 1 REMARK REVDAT 3 19-JUL-23 8AZS 1 JRNL REVDAT 2 24-MAY-23 8AZS 1 JRNL REVDAT 1 02-NOV-22 8AZS 0 JRNL AUTH A.M.STERN,Y.YANG,S.JIN,K.YAMASHITA,A.L.MEUNIER,W.LIU,Y.CAI, JRNL AUTH 2 M.ERICSSON,L.LIU,M.GOEDERT,S.H.W.SCHERES,D.J.SELKOE JRNL TITL ABUNDANT A BETA FIBRILS IN ULTRACENTRIFUGAL SUPERNATANTS OF JRNL TITL 2 AQUEOUS EXTRACTS FROM ALZHEIMER'S DISEASE BRAINS. JRNL REF NEURON V. 111 2012 2023 JRNL REFN ISSN 0896-6273 JRNL PMID 37167969 JRNL DOI 10.1016/J.NEURON.2023.04.007 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : COOT, RELION, REFMAC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7Q4B 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) : 2.900 REMARK 3 NUMBER OF PARTICLES : 37380 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 8AZS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125005. 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 : TYPE I AMYLOID-BETA 42 REMARK 245 FILAMENTS IN SOLUBLE HIGH- REMARK 245 MOLECULAR WEIGHT AGGREGATE REMARK 245 FRACTIONS EXTRACTED FROM REMARK 245 ALZHEIMER'S DISEASE BRAIN 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) : 2400.00 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: H REMARK 350 BIOMT1 1 0.998785 -0.049286 0.000000 5.37167 REMARK 350 BIOMT2 1 0.049286 0.998785 0.000000 -5.11314 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -4.80600 REMARK 350 BIOMT1 2 -0.998785 0.049286 0.000000 207.36433 REMARK 350 BIOMT2 2 -0.049286 -0.998785 0.000000 217.84914 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -4.80600 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 212.73600 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 212.73600 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.998785 0.049286 0.000000 -5.11314 REMARK 350 BIOMT2 5 -0.049286 0.998785 0.000000 5.37167 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 4.80600 REMARK 350 BIOMT1 6 -0.998785 -0.049286 0.000000 217.84914 REMARK 350 BIOMT2 6 0.049286 -0.998785 0.000000 207.36433 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 4.80600 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15770 RELATED DB: EMDB REMARK 900 TYPE I AMYLOID-BETA 42 FILAMENTS IN SOLUBLE HIGH-MOLECULAR WEIGHT REMARK 900 AGGREGATE FRACTIONS EXTRACTED FROM ALZHEIMER'S DISEASE BRAIN DBREF 8AZS H 1 42 UNP P05067 A4_HUMAN 672 713 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 GLU 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 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 0.998529 -0.054218 0.000000 5.92354 MTRIX2 2 0.054218 0.998529 0.000000 -5.61063 MTRIX3 2 0.000000 0.000000 1.000000 -4.79488 MTRIX1 3 -0.999632 0.027119 0.000000 209.81227 MTRIX2 3 -0.027119 -0.999632 0.000000 215.58147 MTRIX3 3 0.000000 0.000000 1.000000 -2.39744 MTRIX1 4 -0.999632 -0.027119 0.000000 215.58147 MTRIX2 4 0.027119 -0.999632 0.000000 209.81227 MTRIX3 4 0.000000 0.000000 1.000000 2.39744 MTRIX1 5 0.998529 0.054218 0.000000 -5.61063 MTRIX2 5 -0.054218 0.998529 0.000000 5.92354 MTRIX3 5 0.000000 0.000000 1.000000 4.79488 MTRIX1 6 -0.996692 -0.081277 0.000000 221.02940 MTRIX2 6 0.081277 -0.996692 0.000000 203.73875 MTRIX3 6 0.000000 0.000000 1.000000 7.19232