HEADER PROTEIN FIBRIL 07-DEC-22 8FF3 TITLE AMYLOID-BETA (1-40) FIBRILS DERIVED FROM FAMILIAL DUTCH-TYPE CAA TITLE 2 PATIENT (POPULATION B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: b, C, a, c, A, B; 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, VASCULAR, FIBRIL, HUMAN, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR E.J.CROOKS,Z.FU,S.CHOWDURY,S.O.SMITH REVDAT 3 01-MAY-24 8FF3 1 JRNL REVDAT 2 24-APR-24 8FF3 1 JRNL REVDAT 1 06-DEC-23 8FF3 0 JRNL AUTH Z.FU,E.J.CROOKS,B.A.IRIZARRY,X.ZHU,S.CHOWDHURY, JRNL AUTH 2 W.E.VAN NOSTRAND,S.O.SMITH JRNL TITL AN ELECTROSTATIC CLUSTER GUIDES A BETA 40 FIBRIL FORMATION JRNL TITL 2 IN SPORADIC AND DUTCH-TYPE CEREBRAL AMYLOID ANGIOPATHY. JRNL REF J.STRUCT.BIOL. V. 216 08092 2024 JRNL REFN ESSN 1095-8657 JRNL PMID 38615725 JRNL DOI 10.1016/J.JSB.2024.108092 REMARK 2 REMARK 2 RESOLUTION. 3.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, GCTF, RELION, COOT, RELION, REMARK 3 RELION, RELION, RELION, PHENIX, ISOLDE REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6W0O REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : 71.700 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) : 3.090 REMARK 3 NUMBER OF PARTICLES : 73287 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 8FF3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270447. 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 : FIBRILLAR ASSEMBLY OF HUMAN REMARK 245 AMYLOID-BETA 1-40 FROM A REMARK 245 FAMILIAL DUTCH-TYPE CEREBRAL REMARK 245 AMYLOID ANGIOPATHY PATIENT 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 : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2140 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1400.00 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) : 5692.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 92000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = 179.75 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 2.44 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: b, C, a, c, A, B 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. (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 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 GLU b 11 REMARK 465 VAL b 12 REMARK 465 HIS b 13 REMARK 465 HIS b 14 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 465 VAL C 12 REMARK 465 HIS C 13 REMARK 465 HIS C 14 REMARK 465 VAL C 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 VAL a 12 REMARK 465 HIS a 13 REMARK 465 HIS a 14 REMARK 465 VAL a 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 465 VAL c 12 REMARK 465 HIS c 13 REMARK 465 HIS c 14 REMARK 465 VAL c 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 VAL A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 VAL A 40 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 GLU B 11 REMARK 465 VAL B 12 REMARK 465 HIS B 13 REMARK 465 HIS B 14 REMARK 465 VAL B 40 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29037 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-29038 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-29036 RELATED DB: EMDB DBREF 8FF3 b 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 8FF3 C 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 8FF3 a 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 8FF3 c 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 8FF3 A 1 40 UNP P05067 A4_HUMAN 653 692 DBREF 8FF3 B 1 40 UNP P05067 A4_HUMAN 653 692 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 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 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 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 SHEET 1 AA1 3 LYS a 16 VAL a 24 0 SHEET 2 AA1 3 LYS b 16 VAL b 24 1 N PHE b 20 O PHE a 19 SHEET 3 AA1 3 LYS c 16 VAL c 24 1 O PHE c 20 N PHE b 19 SHEET 1 AA2 3 ASN a 27 LYS a 28 0 SHEET 2 AA2 3 ASN b 27 LYS b 28 1 N LYS b 28 O ASN a 27 SHEET 3 AA2 3 ASN c 27 LYS c 28 1 O LYS c 28 N ASN b 27 SHEET 1 AA3 3 ILE a 31 VAL a 36 0 SHEET 2 AA3 3 ILE b 31 VAL b 36 1 N ILE b 32 O ILE a 31 SHEET 3 AA3 3 ILE c 31 VAL c 36 1 O ILE c 32 N ILE b 31 SHEET 1 AA4 3 LYS C 16 VAL C 24 0 SHEET 2 AA4 3 LYS B 16 VAL B 24 1 O PHE B 19 N PHE C 20 SHEET 3 AA4 3 LYS A 16 VAL A 24 1 N PHE A 19 O PHE B 20 SHEET 1 AA5 3 ILE C 31 ILE C 32 0 SHEET 2 AA5 3 ILE B 31 ILE B 32 1 O ILE B 31 N ILE C 32 SHEET 3 AA5 3 ILE A 31 ILE A 32 1 N ILE A 31 O ILE B 32 SHEET 1 AA6 3 MET C 35 VAL C 36 0 SHEET 2 AA6 3 MET B 35 VAL B 36 1 O VAL B 36 N MET C 35 SHEET 3 AA6 3 MET A 35 VAL A 36 1 N VAL A 36 O MET B 35 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