HEADER PROTEIN FIBRIL 22-APR-25 9OBK TITLE A-BETA42-MET-R-SO AMYLOIDAL FIBRIL 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 SYNONYM: APP,ABPP,APPI,ALZHEIMER DISEASE AMYLOID A4 PROTEIN HOMOLOG, COMPND 5 ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID PRECURSOR PROTEIN,AMYLOID- COMPND 6 BETA (A4) PRECURSOR PROTEIN,AMYLOID-BETA A4 PROTEIN,CEREBRAL VASCULAR COMPND 7 AMYLOID 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 OXIDIZED, ABETA FILAMENTS, METHIONINE SULFOXIDE, HELICAL KEYWDS 2 RECONSTRUCTION, STEREO-SPECIFIC, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR K.L.CHAN,D.BOYER,V.H.BALASCO SERRAO,J.A.RASKATOV REVDAT 1 06-MAY-26 9OBK 0 JRNL AUTH K.L.CHAN,D.BOYER,V.H.BALASCO SERRAO,J.A.RASKATOV JRNL TITL IMPACT OF STEREOSPECIFIC METHIONINE OXIDATION ON A-BETA 42 JRNL TITL 2 FIBRIL STRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, COOT, PHENIX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 8EZE REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT 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) : 3.010 REMARK 3 NUMBER OF PARTICLES : 200326 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 9OBK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-25. REMARK 100 THE DEPOSITION ID IS D_1000295206. 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 : ABETA-42-MET35-(R)-SO REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.00 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 : 5080 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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) : 3661.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 135000 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: DECAMERIC 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70294 RELATED DB: EMDB REMARK 900 A-BETA42-MET-R-SO AMYLOIDAL FIBRIL REMARK 900 RELATED ID: EMD-70637 RELATED DB: EMDB REMARK 900 ABETA-42-MET35-(R)-SO - CLASS2 REMARK 900 RELATED ID: EMD-70636 RELATED DB: EMDB REMARK 900 A-BETA42-MET-R-SO AMYLOIDAL FIBRIL - CLASS3 DBREF 9OBK A 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK B 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK C 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK D 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK E 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK F 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK G 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK H 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK I 14 41 UNP P05067 A4_HUMAN 685 712 DBREF 9OBK J 14 41 UNP P05067 A4_HUMAN 685 712 SEQRES 1 A 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 A 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 A 28 VAL ILE SEQRES 1 B 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 B 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 B 28 VAL ILE SEQRES 1 C 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 C 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 C 28 VAL ILE SEQRES 1 D 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 D 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 D 28 VAL ILE SEQRES 1 E 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 E 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 E 28 VAL ILE SEQRES 1 F 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 F 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 F 28 VAL ILE SEQRES 1 G 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 G 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 G 28 VAL ILE SEQRES 1 H 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 H 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 H 28 VAL ILE SEQRES 1 I 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 I 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 I 28 VAL ILE SEQRES 1 J 28 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 2 J 28 ASN LYS GLY ALA ILE ILE GLY LEU SME VAL GLY GLY VAL SEQRES 3 J 28 VAL ILE MODRES 9OBK SME A 35 MET MODIFIED RESIDUE MODRES 9OBK SME B 35 MET MODIFIED RESIDUE MODRES 9OBK SME C 35 MET MODIFIED RESIDUE MODRES 9OBK SME D 35 MET MODIFIED RESIDUE MODRES 9OBK SME E 35 MET MODIFIED RESIDUE MODRES 9OBK SME F 35 MET MODIFIED RESIDUE MODRES 9OBK SME G 35 MET MODIFIED RESIDUE MODRES 9OBK SME H 35 MET MODIFIED RESIDUE MODRES 9OBK SME I 35 MET MODIFIED RESIDUE MODRES 9OBK SME J 35 MET MODIFIED RESIDUE HET SME A 35 9 HET SME B 35 9 HET SME C 35 9 HET SME D 35 9 HET SME E 35 9 HET SME F 35 9 HET SME G 35 9 HET SME H 35 9 HET SME I 35 9 HET SME J 35 9 HETNAM SME METHIONINE SULFOXIDE FORMUL 1 SME 10(C5 H11 N O3 S) SHEET 1 AA1 5 LYS H 16 PHE H 19 0 SHEET 2 AA1 5 LYS D 16 PHE D 19 1 N PHE D 19 O VAL H 18 SHEET 3 AA1 5 LYS A 16 PHE A 19 1 N PHE A 19 O VAL D 18 SHEET 4 AA1 5 LYS E 16 PHE E 19 1 O PHE E 19 N VAL A 18 SHEET 5 AA1 5 LYS I 16 PHE I 19 1 O PHE I 19 N VAL E 18 SHEET 1 AA2 5 ILE H 31 VAL H 36 0 SHEET 2 AA2 5 ILE D 31 VAL D 36 1 N GLY D 33 O LEU H 34 SHEET 3 AA2 5 ILE A 31 VAL A 36 1 N GLY A 33 O LEU D 34 SHEET 4 AA2 5 ILE E 31 VAL E 36 1 O GLY E 33 N LEU A 34 SHEET 5 AA2 5 ILE I 31 VAL I 36 1 O GLY I 33 N LEU E 34 SHEET 1 AA3 5 VAL H 39 VAL H 40 0 SHEET 2 AA3 5 VAL D 39 VAL D 40 1 N VAL D 40 O VAL H 39 SHEET 3 AA3 5 VAL A 39 VAL A 40 1 N VAL A 40 O VAL D 39 SHEET 4 AA3 5 VAL E 39 VAL E 40 1 O VAL E 40 N VAL A 39 SHEET 5 AA3 5 VAL I 39 VAL I 40 1 O VAL I 40 N VAL E 39 SHEET 1 AA4 5 LYS G 16 PHE G 19 0 SHEET 2 AA4 5 LYS C 16 PHE C 19 1 N VAL C 18 O PHE G 19 SHEET 3 AA4 5 LYS B 16 PHE B 19 1 N VAL B 18 O PHE C 19 SHEET 4 AA4 5 LYS F 16 PHE F 19 1 O VAL F 18 N PHE B 19 SHEET 5 AA4 5 LYS J 16 PHE J 19 1 O VAL J 18 N PHE F 19 SHEET 1 AA5 5 ILE G 31 VAL G 36 0 SHEET 2 AA5 5 ILE C 31 VAL C 36 1 N LEU C 34 O GLY G 33 SHEET 3 AA5 5 ILE B 31 VAL B 36 1 N LEU B 34 O GLY C 33 SHEET 4 AA5 5 ILE F 31 VAL F 36 1 O LEU F 34 N GLY B 33 SHEET 5 AA5 5 ILE J 31 VAL J 36 1 O LEU J 34 N GLY F 33 SHEET 1 AA6 5 VAL G 39 VAL G 40 0 SHEET 2 AA6 5 VAL C 39 VAL C 40 1 N VAL C 39 O VAL G 40 SHEET 3 AA6 5 VAL B 39 VAL B 40 1 N VAL B 39 O VAL C 40 SHEET 4 AA6 5 VAL F 39 VAL F 40 1 O VAL F 39 N VAL B 40 SHEET 5 AA6 5 VAL J 39 VAL J 40 1 O VAL J 39 N VAL F 40 LINK C LEU A 34 N SME A 35 1555 1555 1.33 LINK C SME A 35 N VAL A 36 1555 1555 1.33 LINK C LEU B 34 N SME B 35 1555 1555 1.33 LINK C SME B 35 N VAL B 36 1555 1555 1.33 LINK C LEU C 34 N SME C 35 1555 1555 1.33 LINK C SME C 35 N VAL C 36 1555 1555 1.33 LINK C LEU D 34 N SME D 35 1555 1555 1.33 LINK C SME D 35 N VAL D 36 1555 1555 1.33 LINK C LEU E 34 N SME E 35 1555 1555 1.33 LINK C SME E 35 N VAL E 36 1555 1555 1.33 LINK C LEU F 34 N SME F 35 1555 1555 1.33 LINK C SME F 35 N VAL F 36 1555 1555 1.33 LINK C LEU G 34 N SME G 35 1555 1555 1.33 LINK C SME G 35 N VAL G 36 1555 1555 1.33 LINK C LEU H 34 N SME H 35 1555 1555 1.33 LINK C SME H 35 N VAL H 36 1555 1555 1.33 LINK C LEU I 34 N SME I 35 1555 1555 1.33 LINK C SME I 35 N VAL I 36 1555 1555 1.33 LINK C LEU J 34 N SME J 35 1555 1555 1.33 LINK C SME J 35 N VAL J 36 1555 1555 1.33 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 CONECT 153 159 CONECT 159 153 160 CONECT 160 159 161 166 CONECT 161 160 162 CONECT 162 161 163 CONECT 163 162 164 165 CONECT 164 163 CONECT 165 163 CONECT 166 160 167 168 CONECT 167 166 CONECT 168 166 CONECT 358 364 CONECT 364 358 365 CONECT 365 364 366 371 CONECT 366 365 367 CONECT 367 366 368 CONECT 368 367 369 370 CONECT 369 368 CONECT 370 368 CONECT 371 365 372 373 CONECT 372 371 CONECT 373 371 CONECT 563 569 CONECT 569 563 570 CONECT 570 569 571 576 CONECT 571 570 572 CONECT 572 571 573 CONECT 573 572 574 575 CONECT 574 573 CONECT 575 573 CONECT 576 570 577 578 CONECT 577 576 CONECT 578 576 CONECT 768 774 CONECT 774 768 775 CONECT 775 774 776 781 CONECT 776 775 777 CONECT 777 776 778 CONECT 778 777 779 780 CONECT 779 778 CONECT 780 778 CONECT 781 775 782 783 CONECT 782 781 CONECT 783 781 CONECT 973 979 CONECT 979 973 980 CONECT 980 979 981 986 CONECT 981 980 982 CONECT 982 981 983 CONECT 983 982 984 985 CONECT 984 983 CONECT 985 983 CONECT 986 980 987 988 CONECT 987 986 CONECT 988 986 CONECT 1178 1184 CONECT 1184 1178 1185 CONECT 1185 1184 1186 1191 CONECT 1186 1185 1187 CONECT 1187 1186 1188 CONECT 1188 1187 1189 1190 CONECT 1189 1188 CONECT 1190 1188 CONECT 1191 1185 1192 1193 CONECT 1192 1191 CONECT 1193 1191 CONECT 1383 1389 CONECT 1389 1383 1390 CONECT 1390 1389 1391 1396 CONECT 1391 1390 1392 CONECT 1392 1391 1393 CONECT 1393 1392 1394 1395 CONECT 1394 1393 CONECT 1395 1393 CONECT 1396 1390 1397 1398 CONECT 1397 1396 CONECT 1398 1396 CONECT 1588 1594 CONECT 1594 1588 1595 CONECT 1595 1594 1596 1601 CONECT 1596 1595 1597 CONECT 1597 1596 1598 CONECT 1598 1597 1599 1600 CONECT 1599 1598 CONECT 1600 1598 CONECT 1601 1595 1602 1603 CONECT 1602 1601 CONECT 1603 1601 CONECT 1793 1799 CONECT 1799 1793 1800 CONECT 1800 1799 1801 1806 CONECT 1801 1800 1802 CONECT 1802 1801 1803 CONECT 1803 1802 1804 1805 CONECT 1804 1803 CONECT 1805 1803 CONECT 1806 1800 1807 1808 CONECT 1807 1806 CONECT 1808 1806 CONECT 1998 2004 CONECT 2004 1998 2005 CONECT 2005 2004 2006 2011 CONECT 2006 2005 2007 CONECT 2007 2006 2008 CONECT 2008 2007 2009 2010 CONECT 2009 2008 CONECT 2010 2008 CONECT 2011 2005 2012 2013 CONECT 2012 2011 CONECT 2013 2011 MASTER 104 0 10 0 30 0 0 6 2040 10 110 30 END