HEADER PROTEIN FIBRIL 06-MAY-25 9OII TITLE STRUCTURE OF TYPE III ABRI AMYLOID FILAMENTS EXTRACTED FROM HUMAN TITLE 2 BRAIN OF FAMILIAL BRITISH DEMENTIA PATIENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABRI (ITM2B MUTANT); COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O 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 9OII 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. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 62238 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 9OII 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_1000295666. 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: 15-MERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: 15-MERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, L, M, N, O 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 2 REMARK 465 ASN A 34 REMARK 465 ILE B 30 REMARK 465 ILE B 31 REMARK 465 GLU B 32 REMARK 465 GLU B 33 REMARK 465 ASN B 34 REMARK 465 ALA C 2 REMARK 465 ALA D 2 REMARK 465 ASN D 34 REMARK 465 ILE E 30 REMARK 465 ILE E 31 REMARK 465 GLU E 32 REMARK 465 GLU E 33 REMARK 465 ASN E 34 REMARK 465 ALA F 2 REMARK 465 ALA G 2 REMARK 465 ASN G 34 REMARK 465 ILE H 30 REMARK 465 ILE H 31 REMARK 465 GLU H 32 REMARK 465 GLU H 33 REMARK 465 ASN H 34 REMARK 465 ALA I 2 REMARK 465 ALA J 2 REMARK 465 ASN J 34 REMARK 465 ILE K 30 REMARK 465 ILE K 31 REMARK 465 GLU K 32 REMARK 465 GLU K 33 REMARK 465 ASN K 34 REMARK 465 ALA L 2 REMARK 465 ALA M 2 REMARK 465 ASN M 34 REMARK 465 ILE N 30 REMARK 465 ILE N 31 REMARK 465 GLU N 32 REMARK 465 GLU N 33 REMARK 465 ASN N 34 REMARK 465 ALA O 2 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 PHE A 6 -172.34 56.63 REMARK 500 ASN A 13 37.57 -97.75 REMARK 500 VAL A 17 -61.23 -127.76 REMARK 500 VAL B 17 -49.06 -130.73 REMARK 500 PHE D 6 -172.38 56.72 REMARK 500 ASN D 13 37.63 -97.82 REMARK 500 VAL D 17 -61.27 -127.74 REMARK 500 ASN D 29 70.05 57.77 REMARK 500 VAL E 17 -49.03 -130.75 REMARK 500 PHE G 6 -172.33 56.61 REMARK 500 ASN G 13 37.50 -97.74 REMARK 500 VAL G 17 -61.27 -127.76 REMARK 500 VAL H 17 -49.06 -130.75 REMARK 500 PHE J 6 -172.34 56.62 REMARK 500 ASN J 13 37.60 -97.74 REMARK 500 VAL J 17 -61.30 -127.82 REMARK 500 ASN J 29 70.01 57.77 REMARK 500 VAL K 17 -49.08 -130.84 REMARK 500 PHE M 6 -172.25 56.63 REMARK 500 ASN M 13 37.53 -97.80 REMARK 500 VAL M 17 -61.22 -127.79 REMARK 500 VAL N 17 -49.10 -130.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-70524 RELATED DB: EMDB REMARK 900 STRUCTURE OF TYPE III ABRI AMYLOID FILAMENTS EXTRACTED FROM HUMAN REMARK 900 BRAIN OF FAMILIAL BRITISH DEMENTIA PATIENT DBREF 9OII A 2 34 PDB 9OII 9OII 2 34 DBREF 9OII B 2 34 PDB 9OII 9OII 2 34 DBREF 9OII C 2 34 PDB 9OII 9OII 2 34 DBREF 9OII D 2 34 PDB 9OII 9OII 2 34 DBREF 9OII E 2 34 PDB 9OII 9OII 2 34 DBREF 9OII F 2 34 PDB 9OII 9OII 2 34 DBREF 9OII G 2 34 PDB 9OII 9OII 2 34 DBREF 9OII H 2 34 PDB 9OII 9OII 2 34 DBREF 9OII I 2 34 PDB 9OII 9OII 2 34 DBREF 9OII J 2 34 PDB 9OII 9OII 2 34 DBREF 9OII K 2 34 PDB 9OII 9OII 2 34 DBREF 9OII L 2 34 PDB 9OII 9OII 2 34 DBREF 9OII M 2 34 PDB 9OII 9OII 2 34 DBREF 9OII N 2 34 PDB 9OII 9OII 2 34 DBREF 9OII O 2 34 PDB 9OII 9OII 2 34 SEQRES 1 A 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 A 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 A 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 B 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 B 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 B 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 C 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 C 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 C 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 D 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 D 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 D 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 E 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 E 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 E 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 F 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 F 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 F 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 G 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 G 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 G 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 H 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 H 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 H 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 I 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 I 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 I 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 J 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 J 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 J 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 K 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 K 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 K 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 L 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 L 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 L 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 M 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 M 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 M 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 N 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 N 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 N 33 LYS ASN ILE ILE GLU GLU ASN SEQRES 1 O 33 ALA SER ASN CYS PHE ALA ILE ARG HIS PHE GLU ASN LYS SEQRES 2 O 33 PHE ALA VAL GLU THR LEU ILE CYS SER ARG THR VAL LYS SEQRES 3 O 33 LYS ASN ILE ILE GLU GLU ASN SHEET 1 AA1 5 LEU G 20 ILE G 21 0 SHEET 2 AA1 5 LEU D 20 ILE D 21 1 N LEU D 20 O ILE G 21 SHEET 3 AA1 5 LEU A 20 ILE A 21 1 N LEU A 20 O ILE D 21 SHEET 4 AA1 5 LEU J 20 ILE J 21 1 O LEU J 20 N ILE A 21 SHEET 5 AA1 5 LEU M 20 ILE M 21 1 O LEU M 20 N ILE J 21 SHEET 1 AA2 5 ARG G 24 LYS G 27 0 SHEET 2 AA2 5 ARG D 24 ILE D 30 1 N THR D 25 O VAL G 26 SHEET 3 AA2 5 ARG A 24 ILE A 31 1 N THR A 25 O VAL D 26 SHEET 4 AA2 5 ARG J 24 ILE J 31 1 O LYS J 27 N VAL A 26 SHEET 5 AA2 5 ARG M 24 ILE M 31 1 O THR M 25 N VAL J 26 SHEET 1 AA3 5 SER H 3 CYS H 5 0 SHEET 2 AA3 5 SER E 3 CYS E 5 1 N CYS E 5 O ASN H 4 SHEET 3 AA3 5 SER B 3 CYS B 5 1 N CYS B 5 O ASN E 4 SHEET 4 AA3 5 SER K 3 CYS K 5 1 O CYS K 5 N ASN B 4 SHEET 5 AA3 5 SER N 3 CYS N 5 1 O CYS N 5 N ASN K 4 SHEET 1 AA4 5 VAL H 26 LYS H 27 0 SHEET 2 AA4 5 VAL E 26 LYS E 27 1 N VAL E 26 O LYS H 27 SHEET 3 AA4 5 VAL B 26 LYS B 27 1 N VAL B 26 O LYS E 27 SHEET 4 AA4 5 ARG K 24 LYS K 27 1 O VAL K 26 N LYS B 27 SHEET 5 AA4 5 ARG N 24 LYS N 27 1 O VAL N 26 N THR K 25 SHEET 1 AA5 5 ASN F 4 CYS F 5 0 SHEET 2 AA5 5 ASN C 4 CYS C 5 1 N ASN C 4 O CYS F 5 SHEET 3 AA5 5 ASN O 4 CYS O 5 1 O ASN O 4 N CYS C 5 SHEET 4 AA5 5 ASN I 4 CYS I 5 1 N ASN I 4 O CYS O 5 SHEET 5 AA5 5 ASN L 4 CYS L 5 1 O ASN L 4 N CYS I 5 SHEET 1 AA6 5 PHE F 11 LYS F 14 0 SHEET 2 AA6 5 PHE C 11 LYS C 14 1 N GLU C 12 O ASN F 13 SHEET 3 AA6 5 PHE O 11 LYS O 14 1 O GLU O 12 N PHE C 11 SHEET 4 AA6 5 PHE I 11 LYS I 14 1 N GLU I 12 O PHE O 11 SHEET 5 AA6 5 PHE L 11 LYS L 14 1 O GLU L 12 N PHE I 11 SHEET 1 AA7 5 VAL F 17 ILE F 21 0 SHEET 2 AA7 5 VAL C 17 ILE C 21 1 N LEU C 20 O THR F 19 SHEET 3 AA7 5 THR O 19 ILE O 21 1 O LEU O 20 N THR C 19 SHEET 4 AA7 5 THR I 19 ILE I 21 1 N LEU I 20 O THR O 19 SHEET 5 AA7 5 THR L 19 ILE L 21 1 O LEU L 20 N THR I 19 SHEET 1 AA8 5 VAL F 26 GLU F 33 0 SHEET 2 AA8 5 VAL C 26 GLU C 33 1 N ILE C 30 O ILE F 31 SHEET 3 AA8 5 VAL O 26 GLU O 33 1 O ILE O 30 N ILE C 31 SHEET 4 AA8 5 VAL I 26 GLU I 33 1 N ILE I 30 O ILE O 31 SHEET 5 AA8 5 VAL L 26 GLU L 33 1 O ILE L 30 N ILE I 31 SSBOND 1 CYS A 5 CYS A 22 1555 1555 2.03 SSBOND 2 CYS B 5 CYS B 22 1555 1555 2.03 SSBOND 3 CYS C 5 CYS C 22 1555 1555 2.03 SSBOND 4 CYS D 5 CYS D 22 1555 1555 2.03 SSBOND 5 CYS E 5 CYS E 22 1555 1555 2.03 SSBOND 6 CYS F 5 CYS F 22 1555 1555 2.03 SSBOND 7 CYS G 5 CYS G 22 1555 1555 2.03 SSBOND 8 CYS H 5 CYS H 22 1555 1555 2.03 SSBOND 9 CYS I 5 CYS I 22 1555 1555 2.03 SSBOND 10 CYS J 5 CYS J 22 1555 1555 2.03 SSBOND 11 CYS K 5 CYS K 22 1555 1555 2.03 SSBOND 12 CYS L 5 CYS L 22 1555 1555 2.03 SSBOND 13 CYS M 5 CYS M 22 1555 1555 2.03 SSBOND 14 CYS N 5 CYS N 22 1555 1555 2.03 SSBOND 15 CYS O 5 CYS O 22 1555 1555 2.03 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 280 423 CONECT 423 280 CONECT 501 644 CONECT 644 501 CONECT 765 908 CONECT 908 765 CONECT 1025 1168 CONECT 1168 1025 CONECT 1246 1389 CONECT 1389 1246 CONECT 1510 1653 CONECT 1653 1510 CONECT 1770 1913 CONECT 1913 1770 CONECT 1991 2134 CONECT 2134 1991 CONECT 2255 2398 CONECT 2398 2255 CONECT 2515 2658 CONECT 2658 2515 CONECT 2736 2879 CONECT 2879 2736 CONECT 3000 3143 CONECT 3143 3000 CONECT 3260 3403 CONECT 3403 3260 CONECT 3481 3624 CONECT 3624 3481 MASTER 188 0 0 0 40 0 0 6 3710 15 30 45 END