HEADER PROTEIN FIBRIL 25-SEP-23 8QN6 TITLE AMYLOID-BETA 40 TYPE 2 FILAMENT FROM THE LEPTOMENINGES OF INDIVIDUAL TITLE 2 WITH ALZHEIMER'S DISEASE AND CEREBRAL AMYLOID ANGIOPATHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA A4 PROTEIN; COMPND 3 CHAIN: F, A; COMPND 4 SYNONYM: AMYLOID-BETA 40 PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS AMYLOID-BETA, AMYLOID, FILAMENTS, QUADRUPLET, ABETA40, HUMAN BRAIN, KEYWDS 2 CRYO-EM, ALZHEIMER'S DISEASE, CEREBRAL AMYLOID ANGIOPATHY, PROTEIN KEYWDS 3 FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.YANG,A.S.MURZIN,S.Y.PEAK-CHEW,C.FRANCO,K.L.NEWELL,B.GHETTI, AUTHOR 2 M.GOEDERT,S.H.W.SCHERES REVDAT 3 31-JAN-24 8QN6 1 REMARK REVDAT 2 20-DEC-23 8QN6 1 TITLE COMPND REVDAT 1 13-DEC-23 8QN6 0 JRNL AUTH Y.YANG,A.G.MURZIN,S.PEAK-CHEW,C.FRANCO,H.J.GARRINGER, JRNL AUTH 2 K.L.NEWELL,B.GHETTI,M.GOEDERT,S.H.W.SCHERES JRNL TITL CRYO-EM STRUCTURES OF A BETA 40 FILAMENTS FROM THE JRNL TITL 2 LEPTOMENINGES OF INDIVIDUALS WITH ALZHEIMER'S DISEASE AND JRNL TITL 3 CEREBRAL AMYLOID ANGIOPATHY. JRNL REF ACTA NEUROPATHOL COMMUN V. 11 191 2023 JRNL REFN ESSN 2051-5960 JRNL PMID 38049918 JRNL DOI 10.1186/S40478-023-01694-8 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, RELION, COOT, RELION, REMARK 3 RELION, RELION, 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) : 2.400 REMARK 3 NUMBER OF PARTICLES : 81140 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 8QN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292133557. 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 40 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 : FEI FALCON IV (4K 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: 12-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, A REMARK 350 BIOMT1 1 0.999905 0.013772 0.000000 -1.62816 REMARK 350 BIOMT2 1 -0.013772 0.999905 0.000000 1.65074 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -4.87269 REMARK 350 BIOMT1 2 -0.999905 -0.013772 0.000000 239.70816 REMARK 350 BIOMT2 2 0.013772 -0.999905 0.000000 236.42926 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -4.87269 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 238.08000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 238.08000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 0.999905 -0.013772 0.000000 1.65074 REMARK 350 BIOMT2 5 0.013772 0.999905 0.000000 -1.62816 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 4.87269 REMARK 350 BIOMT1 6 -0.999905 0.013772 0.000000 236.42926 REMARK 350 BIOMT2 6 -0.013772 -0.999905 0.000000 239.70816 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 4.87269 REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, A REMARK 350 BIOMT1 7 -0.999905 -0.013772 0.000000 239.70816 REMARK 350 BIOMT2 7 0.013772 -0.999905 0.000000 236.42926 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -4.87269 REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, A REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, A REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 238.08000 REMARK 350 BIOMT2 9 0.000000 -1.000000 0.000000 238.08000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, A REMARK 350 BIOMT1 10 0.999905 -0.013772 0.000000 1.65074 REMARK 350 BIOMT2 10 0.013772 0.999905 0.000000 -1.62816 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 4.87269 REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, A REMARK 350 BIOMT1 11 -0.999905 0.013772 0.000000 236.42926 REMARK 350 BIOMT2 11 -0.013772 -0.999905 0.000000 239.70816 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 4.87269 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 F 39 REMARK 465 VAL F 40 REMARK 465 VAL A 39 REMARK 465 VAL A 40 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 GLU F 22 -65.86 -107.93 REMARK 500 ASP A 23 65.78 63.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18508 RELATED DB: EMDB REMARK 900 AMYLOID-BETA 40 QUADRUPLET FILAMENT FROM THE LEPTOMENINGES OF REMARK 900 INDIVIDUALS WITH ALZHEIMER'S DISEASE AND CEREBRAL AMYLOID ANGIOPATHY DBREF 8QN6 F 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 DBREF 8QN6 A 1 40 UNP B4DM00 B4DM00_HUMAN 430 469 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 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 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 0.999905 -0.013772 0.000000 1.65070 MTRIX2 2 0.013772 0.999905 0.000000 -1.62820 MTRIX3 2 0.000000 0.000000 1.000000 4.87270 MTRIX1 3 -0.999905 0.013772 0.000000 236.42930 MTRIX2 3 -0.013772 -0.999905 0.000000 239.70820 MTRIX3 3 0.000000 0.000000 1.000000 4.87270 MTRIX1 4 0.999905 0.013772 0.000000 -1.62820 MTRIX2 4 -0.013772 0.999905 0.000000 1.65070 MTRIX3 4 0.000000 0.000000 1.000000 -4.87270 MTRIX1 5 -1.000000 0.000000 0.000000 238.08000 MTRIX2 5 0.000000 -1.000000 0.000000 238.08000 MTRIX3 5 0.000000 0.000000 1.000000 0.00000