HEADER PROTEIN FIBRIL 02-MAR-20 6W0O TITLE AMYLOID-BETA(1-40) FIBRIL DERIVED FROM ALZHEIMER'S DISEASE CORTICAL TITLE 2 TISSUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: 1, 2, 3, 4, 5, 6; COMPND 4 FRAGMENT: UNP RESIDUES 653-692; COMPND 5 SYNONYM: APP,ABPP,APPI,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 6 PRECURSOR PROTEIN,AMYLOID-BETA A4 PROTEIN,CEREBRAL VASCULAR AMYLOID COMPND 7 PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID-BETA, ALZHEIMER'S DISEASE, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY; SOLID-STATE NMR NUMMDL 10 AUTHOR U.GHOSH,K.R.THURBER,R.TYCKO REVDAT 3 14-JUN-23 6W0O 1 REMARK REVDAT 2 27-JAN-21 6W0O 1 JRNL REVDAT 1 13-JAN-21 6W0O 0 JRNL AUTH U.GHOSH,K.R.THURBER,W.M.YAU,R.TYCKO JRNL TITL MOLECULAR STRUCTURE OF A PREVALENT AMYLOID-BETA FIBRIL JRNL TITL 2 POLYMORPH FROM ALZHEIMER'S DISEASE BRAIN TISSUE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33431654 JRNL DOI 10.1073/PNAS.2023089118 REMARK 2 REMARK 2 RESOLUTION. 2.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.53 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PHI/PSI FROM TALOSN & EM DENSITY USED REMARK 3 AS RESTRAINTS REMARK 4 REMARK 4 6W0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247143. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 297 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 100 UM U-15N,13C AMYLOID-BETA(1 REMARK 210 -40), PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D NCACX; 3D NCOCX; 3D CANCX; 3D REMARK 210 CONCX; 2D 13C-13C REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INFINITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS. 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(1-40) FIBRILS REMARK 245 DERIVED FROM HUMAN AD BRAIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.45 REMARK 245 SAMPLE SUPPORT DETAILS : THE GRIDS WERE CHECKED IN REMARK 245 MICROSCOPE PRIOR TO USE. REMARK 245 SAMPLE VITRIFICATION DETAILS : THE GRIDS WERE PREBLOTTED FOR REMARK 245 10 SECONDS AND BLOTTED FOR 6 REMARK 245 SECONDS BEFORE PLUNGING. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : FIBRILS PRODUCED BY SEEDED REMARK 245 GROWTH USING AMYLOID-BETA IN BRAIN EXTRACT AS THE SOURCE OF REMARK 245 SEEDS. CRYOEM AND SOLID STATE NMR MEASUREMENTS WERE PERFORMED ON REMARK 245 SECOND-GENERATION SEEDED FIBRILS. REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1337 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : -500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : -3000.00 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) : 7350.00 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 : PRELIMINARY GRID SCREENING REMARK 245 WAS DONE MANUALLY IN FEI T12. 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 179.66 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 2.45 ANGSTROMS 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: 1, 2, 3, 4, 5, 6 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 ASP 1 1 REMARK 465 ALA 1 2 REMARK 465 GLU 1 3 REMARK 465 PHE 1 4 REMARK 465 ARG 1 5 REMARK 465 HIS 1 6 REMARK 465 ASP 1 7 REMARK 465 SER 1 8 REMARK 465 GLY 1 9 REMARK 465 ASP 2 1 REMARK 465 ALA 2 2 REMARK 465 GLU 2 3 REMARK 465 PHE 2 4 REMARK 465 ARG 2 5 REMARK 465 HIS 2 6 REMARK 465 ASP 2 7 REMARK 465 SER 2 8 REMARK 465 GLY 2 9 REMARK 465 ASP 3 1 REMARK 465 ALA 3 2 REMARK 465 GLU 3 3 REMARK 465 PHE 3 4 REMARK 465 ARG 3 5 REMARK 465 HIS 3 6 REMARK 465 ASP 3 7 REMARK 465 SER 3 8 REMARK 465 GLY 3 9 REMARK 465 ASP 4 1 REMARK 465 ALA 4 2 REMARK 465 GLU 4 3 REMARK 465 PHE 4 4 REMARK 465 ARG 4 5 REMARK 465 HIS 4 6 REMARK 465 ASP 4 7 REMARK 465 SER 4 8 REMARK 465 GLY 4 9 REMARK 465 ASP 5 1 REMARK 465 ALA 5 2 REMARK 465 GLU 5 3 REMARK 465 PHE 5 4 REMARK 465 ARG 5 5 REMARK 465 HIS 5 6 REMARK 465 ASP 5 7 REMARK 465 SER 5 8 REMARK 465 GLY 5 9 REMARK 465 ASP 6 1 REMARK 465 ALA 6 2 REMARK 465 GLU 6 3 REMARK 465 PHE 6 4 REMARK 465 ARG 6 5 REMARK 465 HIS 6 6 REMARK 465 ASP 6 7 REMARK 465 SER 6 8 REMARK 465 GLY 6 9 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 1 VAL 1 12 121.58 -172.15 REMARK 500 1 HIS 1 14 78.00 70.77 REMARK 500 1 ASP 1 23 65.88 61.16 REMARK 500 1 VAL 2 12 121.30 -171.90 REMARK 500 1 HIS 2 14 78.17 70.88 REMARK 500 1 ASP 2 23 65.93 61.09 REMARK 500 1 VAL 3 12 121.17 -172.53 REMARK 500 1 HIS 3 14 77.93 70.99 REMARK 500 1 ASP 3 23 65.99 61.02 REMARK 500 1 ASP 4 23 63.98 60.53 REMARK 500 1 ASP 5 23 63.93 60.61 REMARK 500 1 ASP 6 23 63.91 60.39 REMARK 500 2 VAL 1 12 72.75 59.13 REMARK 500 2 ASP 1 23 65.71 60.71 REMARK 500 2 VAL 2 12 72.59 59.75 REMARK 500 2 ASP 2 23 65.87 60.60 REMARK 500 2 VAL 3 12 72.63 59.12 REMARK 500 2 ASP 3 23 65.59 60.61 REMARK 500 2 ASP 4 23 65.89 61.24 REMARK 500 2 ASP 5 23 65.95 61.25 REMARK 500 2 ASP 6 23 65.67 61.22 REMARK 500 3 VAL 1 12 76.20 62.58 REMARK 500 3 ASP 1 23 68.51 60.10 REMARK 500 3 VAL 2 12 76.21 62.75 REMARK 500 3 ASP 2 23 68.72 60.12 REMARK 500 3 VAL 3 12 76.16 62.48 REMARK 500 3 ASP 3 23 68.45 60.09 REMARK 500 3 ASP 4 23 79.83 62.72 REMARK 500 3 ASP 5 23 79.91 63.00 REMARK 500 3 ASP 6 23 78.69 63.33 REMARK 500 4 HIS 1 13 -61.83 -106.66 REMARK 500 4 HIS 1 14 77.22 50.53 REMARK 500 4 HIS 2 13 -61.80 -106.39 REMARK 500 4 HIS 2 14 77.64 50.54 REMARK 500 4 ASP 2 23 63.65 60.12 REMARK 500 4 HIS 3 13 -61.49 -107.00 REMARK 500 4 HIS 3 14 76.77 50.36 REMARK 500 4 VAL 4 12 83.63 44.20 REMARK 500 4 ASP 4 23 70.06 60.37 REMARK 500 4 VAL 5 12 83.46 44.43 REMARK 500 4 ASP 5 23 70.12 60.54 REMARK 500 4 VAL 6 12 83.11 44.47 REMARK 500 4 ASP 6 23 70.20 60.09 REMARK 500 5 ASP 1 23 64.48 60.63 REMARK 500 5 ASP 2 23 64.70 60.74 REMARK 500 5 ASP 3 23 64.63 60.40 REMARK 500 5 ASP 4 23 65.25 60.94 REMARK 500 5 ASP 5 23 65.29 61.02 REMARK 500 5 ASP 6 23 65.08 60.91 REMARK 500 6 ASP 4 23 69.20 61.36 REMARK 500 REMARK 500 THIS ENTRY HAS 94 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30731 RELATED DB: BMRB REMARK 900 AMYLOID-BETA(1-40) FIBRIL DERIVED FROM ALZHEIMER'S DISEASE CORTICAL REMARK 900 TISSUE REMARK 900 RELATED ID: EMD-21501 RELATED DB: EMDB REMARK 900 AMYLOID-BETA(1-40) FIBRIL DERIVED FROM ALZHEIMER'S DISEASE CORTICAL REMARK 900 TISSUE DBREF 6W0O 1 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 6W0O 2 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 6W0O 3 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 6W0O 4 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 6W0O 5 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 6W0O 6 1 40 UNP P05067 A4_HUMAN 653 692 SEQRES 1 1 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 1 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 1 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 1 40 VAL SEQRES 1 2 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 2 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 2 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 2 40 VAL SEQRES 1 3 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 3 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 3 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 3 40 VAL SEQRES 1 4 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 4 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 4 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 4 40 VAL SEQRES 1 5 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 5 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 5 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 5 40 VAL SEQRES 1 6 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 6 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 6 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 6 40 VAL SHEET 1 AA1 3 GLN 1 15 VAL 1 24 0 SHEET 2 AA1 3 GLN 2 15 VAL 2 24 1 O PHE 2 19 N VAL 1 18 SHEET 3 AA1 3 GLN 3 15 VAL 3 24 1 O PHE 3 19 N VAL 2 18 SHEET 1 AA2 3 ALA 1 30 ILE 1 32 0 SHEET 2 AA2 3 ALA 2 30 ILE 2 32 1 O ILE 2 31 N ILE 1 32 SHEET 3 AA2 3 ALA 3 30 ILE 3 32 1 O ILE 3 31 N ILE 2 32 SHEET 1 AA3 3 MET 1 35 VAL 1 39 0 SHEET 2 AA3 3 MET 2 35 VAL 2 39 1 O VAL 2 36 N MET 1 35 SHEET 3 AA3 3 MET 3 35 VAL 3 39 1 O VAL 3 36 N MET 2 35 SHEET 1 AA4 3 VAL 4 12 VAL 4 24 0 SHEET 2 AA4 3 VAL 5 12 VAL 5 24 1 O PHE 5 19 N VAL 4 18 SHEET 3 AA4 3 VAL 6 12 VAL 6 24 1 O PHE 6 19 N VAL 5 18 SHEET 1 AA5 3 ALA 4 30 VAL 4 36 0 SHEET 2 AA5 3 ALA 5 30 VAL 5 36 1 O ILE 5 31 N ILE 4 32 SHEET 3 AA5 3 ALA 6 30 VAL 6 36 1 O ILE 6 31 N ILE 5 32 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1