HEADER PROTEIN FIBRIL 06-MAY-25 9OIF TITLE STRUCTURE OF TYPE I ABRI AMYLOID FILAMENTS EXTRACTED FROM HUMAN BRAIN TITLE 2 OF FAMILIAL BRITISH DEMENTIA PATIENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABRI (IT2MB MUTANT); COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 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 9OIF 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. 3.10 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) : 3.100 REMARK 3 NUMBER OF PARTICLES : 55053 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 9OIF 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_1000295664. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 9 -63.76 -90.05 REMARK 500 ARG B 9 -63.70 -90.09 REMARK 500 ARG C 9 -63.73 -90.13 REMARK 500 ARG D 9 -63.81 -90.01 REMARK 500 ARG E 9 -63.74 -90.06 REMARK 500 ARG F 9 -63.79 -90.04 REMARK 500 ARG G 9 -63.71 -90.11 REMARK 500 ARG H 9 -63.69 -90.05 REMARK 500 ARG I 9 -63.73 -90.01 REMARK 500 ARG J 9 -63.73 -90.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70522 RELATED DB: EMDB REMARK 900 STRUCTURE OF TYPE I ABRI AMYLOID FILAMENTS EXTRACTED FROM HUMAN REMARK 900 BRAIN OF FAMILIAL BRITISH DEMENTIA PATIENT DBREF 9OIF A 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF B 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF C 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF D 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF E 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF F 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF G 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF H 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF I 3 33 PDB 9OIF 9OIF 3 33 DBREF 9OIF J 3 33 PDB 9OIF 9OIF 3 33 SEQRES 1 A 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 A 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 A 31 ASN ILE ILE GLU GLU SEQRES 1 B 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 B 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 B 31 ASN ILE ILE GLU GLU SEQRES 1 C 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 C 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 C 31 ASN ILE ILE GLU GLU SEQRES 1 D 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 D 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 D 31 ASN ILE ILE GLU GLU SEQRES 1 E 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 E 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 E 31 ASN ILE ILE GLU GLU SEQRES 1 F 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 F 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 F 31 ASN ILE ILE GLU GLU SEQRES 1 G 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 G 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 G 31 ASN ILE ILE GLU GLU SEQRES 1 H 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 H 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 H 31 ASN ILE ILE GLU GLU SEQRES 1 I 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 I 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 I 31 ASN ILE ILE GLU GLU SEQRES 1 J 31 SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS PHE SEQRES 2 J 31 ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS LYS SEQRES 3 J 31 ASN ILE ILE GLU GLU SHEET 1 AA1 5 LEU C 20 ILE C 21 0 SHEET 2 AA1 5 LEU E 20 ILE E 21 1 O LEU E 20 N ILE C 21 SHEET 3 AA1 5 LEU A 20 ILE A 21 1 N LEU A 20 O ILE E 21 SHEET 4 AA1 5 LEU G 20 ILE G 21 1 O LEU G 20 N ILE A 21 SHEET 5 AA1 5 LEU I 20 ILE I 21 1 O LEU I 20 N ILE G 21 SHEET 1 AA2 5 VAL C 26 ILE C 31 0 SHEET 2 AA2 5 VAL E 26 ILE E 31 1 O LYS E 28 N ASN C 29 SHEET 3 AA2 5 VAL A 26 ILE A 31 1 N LYS A 28 O ASN E 29 SHEET 4 AA2 5 VAL G 26 ILE G 31 1 O LYS G 28 N ASN A 29 SHEET 5 AA2 5 LYS I 27 ILE I 31 1 O LYS I 28 N ASN G 29 SHEET 1 AA3 5 LEU B 20 ILE B 21 0 SHEET 2 AA3 5 LEU D 20 ILE D 21 1 O LEU D 20 N ILE B 21 SHEET 3 AA3 5 LEU J 20 ILE J 21 1 O LEU J 20 N ILE D 21 SHEET 4 AA3 5 LEU F 20 ILE F 21 1 N LEU F 20 O ILE J 21 SHEET 5 AA3 5 LEU H 20 ILE H 21 1 O LEU H 20 N ILE F 21 SHEET 1 AA4 5 LYS B 27 ILE B 31 0 SHEET 2 AA4 5 VAL D 26 ILE D 31 1 O LYS D 28 N ASN B 29 SHEET 3 AA4 5 VAL J 26 ILE J 31 1 O LYS J 28 N ASN D 29 SHEET 4 AA4 5 ARG F 24 ILE F 31 1 N LYS F 28 O ASN J 29 SHEET 5 AA4 5 ARG H 24 ILE H 31 1 O LYS H 28 N ASN F 29 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 275 418 CONECT 418 275 CONECT 530 673 CONECT 673 530 CONECT 785 928 CONECT 928 785 CONECT 1040 1183 CONECT 1183 1040 CONECT 1295 1438 CONECT 1438 1295 CONECT 1550 1693 CONECT 1693 1550 CONECT 1805 1948 CONECT 1948 1805 CONECT 2060 2203 CONECT 2203 2060 CONECT 2315 2458 CONECT 2458 2315 MASTER 128 0 0 0 20 0 0 6 2540 10 20 30 END