HEADER PROTEIN FIBRIL 26-MAY-24 9FH2 TITLE CRYO-EM STRUCTURE OF AMYLOID-BETA FIBRILS CARRYING THE UPPSALA TITLE 2 ABETAUPP(1-42)DELTA(19-24) MUTATION - POLYMORPH 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J; COMPND 4 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 FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR M.ZIELINSKI,F.S.PERALTA REYES,L.GREMER,M.PAGNON DE LA VEGA,C.ROEDER, AUTHOR 2 T.V.HEIDLER,S.SYVAENEN,D.WILLBOLD,D.SEHLIN,M.INGELSSON,G.F.SCHROEDER REVDAT 2 22-OCT-25 9FH2 1 JRNL REVDAT 1 11-JUN-25 9FH2 0 JRNL AUTH M.ZIELINSKI,F.S.PERALTA REYES,L.GREMER,S.SOMMERHAGE, JRNL AUTH 2 M.PAGNON DE LA VEGA,C.RODER,T.V.HEIDLER,S.SYVANEN, JRNL AUTH 3 D.WILLBOLD,D.SEHLIN,M.INGELSSON,G.F.SCHRODER JRNL TITL CRYO-EM STUDIES OF AMYLOID-BETA FIBRILS FROM HUMAN AND JRNL TITL 2 MURINE BRAINS CARRYING THE UPPSALA APP MUTATION ( DELTA JRNL TITL 3 690-695). JRNL REF ACTA NEUROPATHOL COMMUN V. 13 209 2025 JRNL REFN ESSN 2051-5960 JRNL PMID 41044681 JRNL DOI 10.1186/S40478-025-02120-X REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, ISOLDE, 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 155170 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 9FH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1292138790. 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 FIBRILS OF AMYLOID REMARK 245 -BETA(1-42)DELTA(19-24) 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 : 2.00 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 TALOS ARCTICA REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 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) : 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 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 A -7 REMARK 465 ALA A -6 REMARK 465 GLU A -5 REMARK 465 PHE A -4 REMARK 465 ARG A -3 REMARK 465 HIS A -2 REMARK 465 ASP A -1 REMARK 465 SER A 0 REMARK 465 ASP B -7 REMARK 465 ALA B -6 REMARK 465 GLU B -5 REMARK 465 PHE B -4 REMARK 465 ARG B -3 REMARK 465 HIS B -2 REMARK 465 ASP B -1 REMARK 465 SER B 0 REMARK 465 ASP C -7 REMARK 465 ALA C -6 REMARK 465 GLU C -5 REMARK 465 PHE C -4 REMARK 465 ARG C -3 REMARK 465 HIS C -2 REMARK 465 ASP C -1 REMARK 465 SER C 0 REMARK 465 ASP D -7 REMARK 465 ALA D -6 REMARK 465 GLU D -5 REMARK 465 PHE D -4 REMARK 465 ARG D -3 REMARK 465 HIS D -2 REMARK 465 ASP D -1 REMARK 465 SER D 0 REMARK 465 ASP E -7 REMARK 465 ALA E -6 REMARK 465 GLU E -5 REMARK 465 PHE E -4 REMARK 465 ARG E -3 REMARK 465 HIS E -2 REMARK 465 ASP E -1 REMARK 465 SER E 0 REMARK 465 ASP F -7 REMARK 465 ALA F -6 REMARK 465 GLU F -5 REMARK 465 PHE F -4 REMARK 465 ARG F -3 REMARK 465 HIS F -2 REMARK 465 ASP F -1 REMARK 465 SER F 0 REMARK 465 ASP G -7 REMARK 465 ALA G -6 REMARK 465 GLU G -5 REMARK 465 PHE G -4 REMARK 465 ARG G -3 REMARK 465 HIS G -2 REMARK 465 ASP G -1 REMARK 465 SER G 0 REMARK 465 ASP H -7 REMARK 465 ALA H -6 REMARK 465 GLU H -5 REMARK 465 PHE H -4 REMARK 465 ARG H -3 REMARK 465 HIS H -2 REMARK 465 ASP H -1 REMARK 465 SER H 0 REMARK 465 ASP I -7 REMARK 465 ALA I -6 REMARK 465 GLU I -5 REMARK 465 PHE I -4 REMARK 465 ARG I -3 REMARK 465 HIS I -2 REMARK 465 ASP I -1 REMARK 465 SER I 0 REMARK 465 ASP J -7 REMARK 465 ALA J -6 REMARK 465 GLU J -5 REMARK 465 PHE J -4 REMARK 465 ARG J -3 REMARK 465 HIS J -2 REMARK 465 ASP J -1 REMARK 465 SER J 0 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50437 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF AMYLOID-BETA FIBRILS CARRYING THE UPPSALA REMARK 900 ABETAUPP(1-42)DELTA(19-24) MUTATION - POLYMORPH 1 DBREF 9FH2 A -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 B -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 C -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 D -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 E -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 F -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 G -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 H -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 I -7 28 UNP P05067 A4_HUMAN 672 713 DBREF 9FH2 J -7 28 UNP P05067 A4_HUMAN 672 713 SEQADV 9FH2 A UNP P05067 VAL 689 DELETION SEQADV 9FH2 A UNP P05067 PHE 690 DELETION SEQADV 9FH2 A UNP P05067 PHE 691 DELETION SEQADV 9FH2 A UNP P05067 ALA 692 DELETION SEQADV 9FH2 A UNP P05067 GLU 693 DELETION SEQADV 9FH2 A UNP P05067 ASP 694 DELETION SEQADV 9FH2 B UNP P05067 VAL 689 DELETION SEQADV 9FH2 B UNP P05067 PHE 690 DELETION SEQADV 9FH2 B UNP P05067 PHE 691 DELETION SEQADV 9FH2 B UNP P05067 ALA 692 DELETION SEQADV 9FH2 B UNP P05067 GLU 693 DELETION SEQADV 9FH2 B UNP P05067 ASP 694 DELETION SEQADV 9FH2 C UNP P05067 VAL 689 DELETION SEQADV 9FH2 C UNP P05067 PHE 690 DELETION SEQADV 9FH2 C UNP P05067 PHE 691 DELETION SEQADV 9FH2 C UNP P05067 ALA 692 DELETION SEQADV 9FH2 C UNP P05067 GLU 693 DELETION SEQADV 9FH2 C UNP P05067 ASP 694 DELETION SEQADV 9FH2 D UNP P05067 VAL 689 DELETION SEQADV 9FH2 D UNP P05067 PHE 690 DELETION SEQADV 9FH2 D UNP P05067 PHE 691 DELETION SEQADV 9FH2 D UNP P05067 ALA 692 DELETION SEQADV 9FH2 D UNP P05067 GLU 693 DELETION SEQADV 9FH2 D UNP P05067 ASP 694 DELETION SEQADV 9FH2 E UNP P05067 VAL 689 DELETION SEQADV 9FH2 E UNP P05067 PHE 690 DELETION SEQADV 9FH2 E UNP P05067 PHE 691 DELETION SEQADV 9FH2 E UNP P05067 ALA 692 DELETION SEQADV 9FH2 E UNP P05067 GLU 693 DELETION SEQADV 9FH2 E UNP P05067 ASP 694 DELETION SEQADV 9FH2 F UNP P05067 VAL 689 DELETION SEQADV 9FH2 F UNP P05067 PHE 690 DELETION SEQADV 9FH2 F UNP P05067 PHE 691 DELETION SEQADV 9FH2 F UNP P05067 ALA 692 DELETION SEQADV 9FH2 F UNP P05067 GLU 693 DELETION SEQADV 9FH2 F UNP P05067 ASP 694 DELETION SEQADV 9FH2 G UNP P05067 VAL 689 DELETION SEQADV 9FH2 G UNP P05067 PHE 690 DELETION SEQADV 9FH2 G UNP P05067 PHE 691 DELETION SEQADV 9FH2 G UNP P05067 ALA 692 DELETION SEQADV 9FH2 G UNP P05067 GLU 693 DELETION SEQADV 9FH2 G UNP P05067 ASP 694 DELETION SEQADV 9FH2 H UNP P05067 VAL 689 DELETION SEQADV 9FH2 H UNP P05067 PHE 690 DELETION SEQADV 9FH2 H UNP P05067 PHE 691 DELETION SEQADV 9FH2 H UNP P05067 ALA 692 DELETION SEQADV 9FH2 H UNP P05067 GLU 693 DELETION SEQADV 9FH2 H UNP P05067 ASP 694 DELETION SEQADV 9FH2 I UNP P05067 VAL 689 DELETION SEQADV 9FH2 I UNP P05067 PHE 690 DELETION SEQADV 9FH2 I UNP P05067 PHE 691 DELETION SEQADV 9FH2 I UNP P05067 ALA 692 DELETION SEQADV 9FH2 I UNP P05067 GLU 693 DELETION SEQADV 9FH2 I UNP P05067 ASP 694 DELETION SEQADV 9FH2 J UNP P05067 VAL 689 DELETION SEQADV 9FH2 J UNP P05067 PHE 690 DELETION SEQADV 9FH2 J UNP P05067 PHE 691 DELETION SEQADV 9FH2 J UNP P05067 ALA 692 DELETION SEQADV 9FH2 J UNP P05067 GLU 693 DELETION SEQADV 9FH2 J UNP P05067 ASP 694 DELETION SEQRES 1 A 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 A 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 B 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 B 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 C 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 C 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 D 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 D 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 E 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 E 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 E 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 F 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 F 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 F 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 G 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 G 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 G 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 H 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 H 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 H 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 I 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 I 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 I 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SEQRES 1 J 36 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 J 36 HIS GLN LYS LEU VAL GLY SER ASN LYS GLY ALA ILE ILE SEQRES 3 J 36 GLY LEU MET VAL GLY GLY VAL VAL ILE ALA SHEET 1 AA1 5 TYR A 2 ASN A 13 0 SHEET 2 AA1 5 TYR C 2 ASN C 13 1 O LYS C 8 N LEU A 9 SHEET 3 AA1 5 TYR E 2 ASN E 13 1 O HIS E 6 N HIS C 5 SHEET 4 AA1 5 TYR G 2 ASN G 13 1 O HIS G 6 N HIS E 5 SHEET 5 AA1 5 TYR I 2 ASN I 13 1 O GLU I 3 N TYR G 2 SHEET 1 AA2 5 ALA A 16 VAL A 22 0 SHEET 2 AA2 5 ALA C 16 VAL C 22 1 O MET C 21 N LEU A 20 SHEET 3 AA2 5 ALA E 16 VAL E 22 1 O MET E 21 N LEU C 20 SHEET 4 AA2 5 ALA G 16 VAL G 22 1 O MET G 21 N LEU E 20 SHEET 5 AA2 5 ALA I 16 VAL I 22 1 O MET I 21 N LEU G 20 SHEET 1 AA3 5 VAL A 25 ILE A 27 0 SHEET 2 AA3 5 VAL C 25 ILE C 27 1 O VAL C 26 N ILE A 27 SHEET 3 AA3 5 VAL E 25 ILE E 27 1 O VAL E 26 N ILE C 27 SHEET 4 AA3 5 VAL G 25 ILE G 27 1 O VAL G 26 N ILE E 27 SHEET 5 AA3 5 VAL I 25 ILE I 27 1 O VAL I 26 N ILE G 27 SHEET 1 AA4 5 TYR B 2 ASN B 13 0 SHEET 2 AA4 5 TYR D 2 ASN D 13 1 O LYS D 8 N LEU B 9 SHEET 3 AA4 5 TYR F 2 ASN F 13 1 O HIS F 6 N HIS D 5 SHEET 4 AA4 5 TYR H 2 ASN H 13 1 O GLU H 3 N TYR F 2 SHEET 5 AA4 5 TYR J 2 ASN J 13 1 O GLU J 3 N TYR H 2 SHEET 1 AA5 5 ALA B 16 VAL B 22 0 SHEET 2 AA5 5 ALA D 16 VAL D 22 1 O MET D 21 N LEU B 20 SHEET 3 AA5 5 ALA F 16 VAL F 22 1 O MET F 21 N LEU D 20 SHEET 4 AA5 5 ALA H 16 VAL H 22 1 O MET H 21 N LEU F 20 SHEET 5 AA5 5 ALA J 16 VAL J 22 1 O MET J 21 N LEU H 20 SHEET 1 AA6 5 VAL B 25 ILE B 27 0 SHEET 2 AA6 5 VAL D 25 ILE D 27 1 O VAL D 26 N ILE B 27 SHEET 3 AA6 5 VAL F 25 ILE F 27 1 O VAL F 26 N ILE D 27 SHEET 4 AA6 5 VAL H 25 ILE H 27 1 O VAL H 26 N ILE F 27 SHEET 5 AA6 5 VAL J 25 ILE J 27 1 O VAL J 26 N ILE H 27 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 MASTER 188 0 0 0 30 0 0 6 1990 10 0 30 END