HEADER PROTEIN FIBRIL 06-MAY-25 9OIP TITLE STRUCTURE OF ABRI AMYLOID FILAMENTS FROM SYNTHESIZED ABRI PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABRI (ITM2B MUTANT); 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_TAXID: 9606 KEYWDS AMYLOID, FILAMENT, NEURODEGENERATION, BRAIN, EX VIVO, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR K.A.OZCAN,F.VAGO,S.R.BHARATH,W.JIANG,R.VIDAL REVDAT 1 27-MAY-26 9OIP 0 JRNL AUTH K.A.OZCAN,F.VAGO,S.R.BHARATH,W.JIANG,R.VIDAL JRNL TITL CRYO-EM STRUCTURES OF ADAN AND ABRI FILAMENTS FROM FDD AND JRNL TITL 2 FBD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 152184 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 9OIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295673. 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 : ABRI AMYLOID FILAMENT 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 : 8.00 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 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 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70525 RELATED DB: EMDB REMARK 900 STRUCTURE OF ABRI AMYLOID FILAMENTS FROM SYNTHESIZED ABRI PEPTIDE DBREF 9OIP A 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP B 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP C 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP D 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP E 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP F 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP G 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP H 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP I 3 34 PDB 9OIP 9OIP 3 34 DBREF 9OIP J 3 34 PDB 9OIP 9OIP 3 34 SEQRES 1 A 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 A 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 A 32 ASN ILE ILE GLU GLU ASN SEQRES 1 B 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 B 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 B 32 ASN ILE ILE GLU GLU ASN SEQRES 1 C 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 C 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 C 32 ASN ILE ILE GLU GLU ASN SEQRES 1 D 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 D 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 D 32 ASN ILE ILE GLU GLU ASN SEQRES 1 E 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 E 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 E 32 ASN ILE ILE GLU GLU ASN SEQRES 1 F 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 F 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 F 32 ASN ILE ILE GLU GLU ASN SEQRES 1 G 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 G 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 G 32 ASN ILE ILE GLU GLU ASN SEQRES 1 H 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 H 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 H 32 ASN ILE ILE GLU GLU ASN SEQRES 1 I 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 I 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 I 32 ASN ILE ILE GLU GLU ASN SEQRES 1 J 32 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 J 32 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 J 32 ASN ILE ILE GLU GLU ASN SHEET 1 AA1 3 PHE A 11 ASN A 13 0 SHEET 2 AA1 3 PHE C 11 ASN C 13 1 O PHE C 11 N GLU A 12 SHEET 3 AA1 3 PHE G 11 ASN G 13 1 O PHE G 11 N GLU C 12 SHEET 1 AA2 5 VAL E 17 CYS E 22 0 SHEET 2 AA2 5 VAL G 17 CYS G 22 1 O ILE G 21 N CYS E 22 SHEET 3 AA2 5 VAL C 17 CYS C 22 1 N ILE C 21 O CYS G 22 SHEET 4 AA2 5 VAL A 17 CYS A 22 1 N ILE A 21 O CYS C 22 SHEET 5 AA2 5 VAL I 17 CYS I 22 1 O VAL I 17 N GLU A 18 SHEET 1 AA3 5 THR E 25 VAL E 26 0 SHEET 2 AA3 5 THR G 25 VAL G 26 1 O VAL G 26 N THR E 25 SHEET 3 AA3 5 THR C 25 VAL C 26 1 N VAL C 26 O THR G 25 SHEET 4 AA3 5 THR A 25 VAL A 26 1 N VAL A 26 O THR C 25 SHEET 5 AA3 5 THR I 25 VAL I 26 1 O VAL I 26 N THR A 25 SHEET 1 AA4 5 ILE E 30 GLU E 33 0 SHEET 2 AA4 5 ILE G 30 GLU G 33 1 O ILE G 31 N ILE E 30 SHEET 3 AA4 5 ILE C 30 GLU C 33 1 N ILE C 31 O ILE G 30 SHEET 4 AA4 5 ILE A 30 GLU A 33 1 N ILE A 31 O ILE C 30 SHEET 5 AA4 5 ILE I 30 GLU I 33 1 O ILE I 31 N ILE A 30 SHEET 1 AA5 2 PHE B 11 ASN B 13 0 SHEET 2 AA5 2 PHE J 11 ASN J 13 1 O GLU J 12 N PHE B 11 SHEET 1 AA6 5 VAL D 17 CYS D 22 0 SHEET 2 AA6 5 VAL F 17 CYS F 22 1 O ILE F 21 N CYS D 22 SHEET 3 AA6 5 VAL B 17 CYS B 22 1 N ILE B 21 O CYS F 22 SHEET 4 AA6 5 VAL J 17 CYS J 22 1 O ILE J 21 N CYS B 22 SHEET 5 AA6 5 VAL H 17 CYS H 22 1 N ILE H 21 O CYS J 22 SHEET 1 AA7 5 THR D 25 VAL D 26 0 SHEET 2 AA7 5 THR F 25 VAL F 26 1 O VAL F 26 N THR D 25 SHEET 3 AA7 5 THR B 25 VAL B 26 1 N VAL B 26 O THR F 25 SHEET 4 AA7 5 THR J 25 VAL J 26 1 O VAL J 26 N THR B 25 SHEET 5 AA7 5 THR H 25 VAL H 26 1 N VAL H 26 O THR J 25 SHEET 1 AA8 5 ILE D 30 GLU D 33 0 SHEET 2 AA8 5 ILE F 30 GLU F 33 1 O ILE F 31 N ILE D 30 SHEET 3 AA8 5 ILE B 30 GLU B 33 1 N ILE B 31 O ILE F 30 SHEET 4 AA8 5 ILE J 30 GLU J 33 1 O ILE J 31 N ILE B 30 SHEET 5 AA8 5 ILE H 30 GLU H 33 1 N ILE H 31 O ILE J 30 SSBOND 1 CYS A 5 CYS A 22 1555 1555 2.04 SSBOND 2 CYS B 5 CYS B 22 1555 1555 2.04 SSBOND 3 CYS C 5 CYS C 22 1555 1555 2.04 SSBOND 4 CYS D 5 CYS D 22 1555 1555 2.04 SSBOND 5 CYS E 5 CYS E 22 1555 1555 2.04 SSBOND 6 CYS F 5 CYS F 22 1555 1555 2.04 SSBOND 7 CYS G 5 CYS G 22 1555 1555 2.04 SSBOND 8 CYS H 5 CYS H 22 1555 1555 2.04 SSBOND 9 CYS I 5 CYS I 22 1555 1555 2.04 SSBOND 10 CYS J 5 CYS J 22 1555 1555 2.04 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 20 163 CONECT 163 20 CONECT 283 426 CONECT 426 283 CONECT 546 689 CONECT 689 546 CONECT 809 952 CONECT 952 809 CONECT 1072 1215 CONECT 1215 1072 CONECT 1335 1478 CONECT 1478 1335 CONECT 1598 1741 CONECT 1741 1598 CONECT 1861 2004 CONECT 2004 1861 CONECT 2124 2267 CONECT 2267 2124 CONECT 2387 2530 CONECT 2530 2387 MASTER 100 0 0 0 35 0 0 6 2620 10 20 30 END