HEADER PROTEIN FIBRIL 14-MAY-25 9ONC TITLE A-BETA42-MET-R-SO AMYLOIDAL FIBRIL - CLASS3 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 20-MAY-26 9ONC 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. 3.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9OBK 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) : 3.640 REMARK 3 NUMBER OF PARTICLES : 22212 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 9ONC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295908. 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 - CLASS3 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 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 ALA A 42 REMARK 465 ALA B 42 REMARK 465 ALA C 42 REMARK 465 ALA D 42 REMARK 465 ALA E 42 REMARK 465 ALA F 42 REMARK 465 ALA G 42 REMARK 465 ALA H 42 REMARK 465 ALA I 42 REMARK 465 ALA J 42 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU B 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU C 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU D 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU E 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU F 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU G 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU H 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU I 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 LEU J 17 O - C - N ANGL. DEV. = -18.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 17 -31.30 REMARK 500 LEU B 17 -31.32 REMARK 500 LEU C 17 -31.31 REMARK 500 LEU D 17 -31.32 REMARK 500 LEU E 17 -31.31 REMARK 500 LEU F 17 -31.35 REMARK 500 LEU G 17 -31.28 REMARK 500 LEU H 17 -31.28 REMARK 500 LEU I 17 -31.29 REMARK 500 LEU J 17 -31.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70294 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-70636 RELATED DB: EMDB REMARK 900 A-BETA42-MET-R-SO AMYLOIDAL FIBRIL - CLASS3 DBREF 9ONC A 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC B 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC C 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC D 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC E 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC F 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC G 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC H 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC I 17 42 UNP P05067 A4_HUMAN 688 713 DBREF 9ONC J 17 42 UNP P05067 A4_HUMAN 688 713 SEQRES 1 A 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 A 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 B 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 B 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 C 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 C 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 D 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 D 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 E 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 E 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 F 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 F 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 G 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 G 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 H 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 H 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 I 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 I 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA SEQRES 1 J 26 LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY SEQRES 2 J 26 ALA ILE ILE GLY LEU SME VAL GLY GLY VAL VAL ILE ALA MODRES 9ONC SME A 35 MET MODIFIED RESIDUE MODRES 9ONC SME B 35 MET MODIFIED RESIDUE MODRES 9ONC SME C 35 MET MODIFIED RESIDUE MODRES 9ONC SME D 35 MET MODIFIED RESIDUE MODRES 9ONC SME E 35 MET MODIFIED RESIDUE MODRES 9ONC SME F 35 MET MODIFIED RESIDUE MODRES 9ONC SME G 35 MET MODIFIED RESIDUE MODRES 9ONC SME H 35 MET MODIFIED RESIDUE MODRES 9ONC SME I 35 MET MODIFIED RESIDUE MODRES 9ONC 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 ILE H 31 SME H 35 0 SHEET 2 AA1 5 ILE D 31 SME D 35 1 N ILE D 32 O GLY H 33 SHEET 3 AA1 5 ILE A 31 SME A 35 1 N ILE A 32 O GLY D 33 SHEET 4 AA1 5 ILE E 31 SME E 35 1 O ILE E 32 N GLY A 33 SHEET 5 AA1 5 ILE I 31 SME I 35 1 O ILE I 32 N GLY E 33 SHEET 1 AA2 5 VAL H 39 VAL H 40 0 SHEET 2 AA2 5 VAL D 39 VAL D 40 1 N VAL D 39 O VAL H 40 SHEET 3 AA2 5 VAL A 39 VAL A 40 1 N VAL A 39 O VAL D 40 SHEET 4 AA2 5 VAL E 39 VAL E 40 1 O VAL E 39 N VAL A 40 SHEET 5 AA2 5 VAL I 39 VAL I 40 1 O VAL I 39 N VAL E 40 SHEET 1 AA3 5 ILE G 31 SME G 35 0 SHEET 2 AA3 5 ILE C 31 SME C 35 1 N GLY C 33 O ILE G 32 SHEET 3 AA3 5 ILE B 31 SME B 35 1 N GLY B 33 O ILE C 32 SHEET 4 AA3 5 ILE F 31 SME F 35 1 O GLY F 33 N ILE B 32 SHEET 5 AA3 5 ILE J 31 SME J 35 1 O GLY J 33 N ILE F 32 SHEET 1 AA4 5 VAL G 39 VAL G 40 0 SHEET 2 AA4 5 VAL C 39 VAL C 40 1 N VAL C 40 O VAL G 39 SHEET 3 AA4 5 VAL B 39 VAL B 40 1 N VAL B 40 O VAL C 39 SHEET 4 AA4 5 VAL F 39 VAL F 40 1 O VAL F 40 N VAL B 39 SHEET 5 AA4 5 VAL J 39 VAL J 40 1 O VAL J 40 N VAL F 39 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 125 131 CONECT 131 125 132 CONECT 132 131 133 138 CONECT 133 132 134 CONECT 134 133 135 CONECT 135 134 136 137 CONECT 136 135 CONECT 137 135 CONECT 138 132 139 140 CONECT 139 138 CONECT 140 138 CONECT 302 308 CONECT 308 302 309 CONECT 309 308 310 315 CONECT 310 309 311 CONECT 311 310 312 CONECT 312 311 313 314 CONECT 313 312 CONECT 314 312 CONECT 315 309 316 317 CONECT 316 315 CONECT 317 315 CONECT 479 485 CONECT 485 479 486 CONECT 486 485 487 492 CONECT 487 486 488 CONECT 488 487 489 CONECT 489 488 490 491 CONECT 490 489 CONECT 491 489 CONECT 492 486 493 494 CONECT 493 492 CONECT 494 492 CONECT 656 662 CONECT 662 656 663 CONECT 663 662 664 669 CONECT 664 663 665 CONECT 665 664 666 CONECT 666 665 667 668 CONECT 667 666 CONECT 668 666 CONECT 669 663 670 671 CONECT 670 669 CONECT 671 669 CONECT 833 839 CONECT 839 833 840 CONECT 840 839 841 846 CONECT 841 840 842 CONECT 842 841 843 CONECT 843 842 844 845 CONECT 844 843 CONECT 845 843 CONECT 846 840 847 848 CONECT 847 846 CONECT 848 846 CONECT 1010 1016 CONECT 1016 1010 1017 CONECT 1017 1016 1018 1023 CONECT 1018 1017 1019 CONECT 1019 1018 1020 CONECT 1020 1019 1021 1022 CONECT 1021 1020 CONECT 1022 1020 CONECT 1023 1017 1024 1025 CONECT 1024 1023 CONECT 1025 1023 CONECT 1187 1193 CONECT 1193 1187 1194 CONECT 1194 1193 1195 1200 CONECT 1195 1194 1196 CONECT 1196 1195 1197 CONECT 1197 1196 1198 1199 CONECT 1198 1197 CONECT 1199 1197 CONECT 1200 1194 1201 1202 CONECT 1201 1200 CONECT 1202 1200 CONECT 1364 1370 CONECT 1370 1364 1371 CONECT 1371 1370 1372 1377 CONECT 1372 1371 1373 CONECT 1373 1372 1374 CONECT 1374 1373 1375 1376 CONECT 1375 1374 CONECT 1376 1374 CONECT 1377 1371 1378 1379 CONECT 1378 1377 CONECT 1379 1377 CONECT 1541 1547 CONECT 1547 1541 1548 CONECT 1548 1547 1549 1554 CONECT 1549 1548 1550 CONECT 1550 1549 1551 CONECT 1551 1550 1552 1553 CONECT 1552 1551 CONECT 1553 1551 CONECT 1554 1548 1555 1556 CONECT 1555 1554 CONECT 1556 1554 CONECT 1718 1724 CONECT 1724 1718 1725 CONECT 1725 1724 1726 1731 CONECT 1726 1725 1727 CONECT 1727 1726 1728 CONECT 1728 1727 1729 1730 CONECT 1729 1728 CONECT 1730 1728 CONECT 1731 1725 1732 1733 CONECT 1732 1731 CONECT 1733 1731 MASTER 168 0 10 0 20 0 0 6 1760 10 110 20 END