HEADER PROTEIN FIBRIL 08-AUG-19 6SHS TITLE ABETA FIBRIL (MORPHOLOGY I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-BETA PRECURSOR PROTEIN; COMPND 3 CHAIN: A, B, C, H, D, I, E, J, F, K, G, L; COMPND 4 SYNONYM: APP,ABPP,APPI,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 5 PRECURSOR PROTEIN,AMYLOID-BETA A4 PROTEIN,CEREBRAL VASCULAR AMYLOID COMPND 6 PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BRAIN; SOURCE 6 TISSUE: MENINGES KEYWDS FIBRIL, BETA AMYLOID, CRYO-EM, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR M.KOLLMER,M.FANDRICH REVDAT 1 06-NOV-19 6SHS 0 JRNL AUTH M.KOLLMER,W.CLOSE,L.FUNK,J.RASMUSSEN,A.BSOUL,A.SCHIERHORN, JRNL AUTH 2 M.SCHMIDT,C.J.SIGURDSON,M.JUCKER,M.FANDRICH JRNL TITL CRYO-EM STRUCTURE AND POLYMORPHISM OF A BETA AMYLOID FIBRILS JRNL TITL 2 PURIFIED FROM ALZHEIMER'S BRAIN TISSUE. JRNL REF NAT COMMUN V. 10 4760 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31664019 JRNL DOI 10.1038/S41467-019-12683-8 REMARK 2 REMARK 2 RESOLUTION. 4.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GCTF, COOT, PHENIX, RELION, RELION, REMARK 3 RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 4.400 REMARK 3 NUMBER OF PARTICLES : 12282 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 6SHS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1292103770. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : MENINGES 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 : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 3027 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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) : 40.90 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 36980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -147.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, H, D, I, E, J, F, K, REMARK 350 AND CHAINS: G, L 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 GLU A 22 -53.60 -121.03 REMARK 500 ALA A 30 -39.44 -131.07 REMARK 500 GLU B 22 -53.57 -121.04 REMARK 500 ALA B 30 -39.46 -131.08 REMARK 500 GLU C 22 -53.56 -121.07 REMARK 500 ALA C 30 -39.41 -131.07 REMARK 500 GLU H 22 -53.53 -121.02 REMARK 500 ALA H 30 -39.47 -131.07 REMARK 500 GLU D 22 -53.58 -121.05 REMARK 500 ALA D 30 -39.39 -131.09 REMARK 500 GLU I 22 -53.56 -121.07 REMARK 500 ALA I 30 -39.49 -131.10 REMARK 500 GLU E 22 -53.61 -121.04 REMARK 500 ALA E 30 -39.44 -131.08 REMARK 500 GLU J 22 -53.58 -121.04 REMARK 500 ALA J 30 -39.47 -131.06 REMARK 500 GLU F 22 -53.62 -121.06 REMARK 500 ALA F 30 -39.47 -131.11 REMARK 500 GLU K 22 -53.63 -121.06 REMARK 500 ALA K 30 -39.49 -131.06 REMARK 500 GLU G 22 -53.64 -121.05 REMARK 500 ALA G 30 -39.44 -131.09 REMARK 500 GLU L 22 -53.60 -121.04 REMARK 500 ALA L 30 -39.46 -131.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4864 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-4866 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-10204 RELATED DB: EMDB REMARK 900 ABETA FIBRIL (MORPHOLOGY I) DBREF 6SHS A 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS B 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS C 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS H 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS D 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS I 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS E 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS J 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS F 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS K 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS G 1 40 UNP P05067 A4_HUMAN 616 655 DBREF 6SHS L 1 40 UNP P05067 A4_HUMAN 616 655 SEQRES 1 A 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 40 VAL SEQRES 1 B 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 B 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 B 40 VAL SEQRES 1 C 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 40 VAL SEQRES 1 H 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 H 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 H 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 H 40 VAL SEQRES 1 D 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 D 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 D 40 VAL SEQRES 1 I 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 I 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 I 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 I 40 VAL SEQRES 1 E 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 E 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 E 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 E 40 VAL SEQRES 1 J 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 J 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 J 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 J 40 VAL SEQRES 1 F 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 F 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 F 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 F 40 VAL SEQRES 1 K 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 K 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 K 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 K 40 VAL SEQRES 1 G 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 G 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 G 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 G 40 VAL SEQRES 1 L 40 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 L 40 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 L 40 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 L 40 VAL SHEET 1 AA1 6 ALA D 2 VAL D 12 0 SHEET 2 AA1 6 ALA C 2 VAL C 12 1 N ASP C 7 O HIS D 6 SHEET 3 AA1 6 ALA A 2 VAL A 12 1 N ASP A 7 O HIS C 6 SHEET 4 AA1 6 ALA E 2 VAL E 12 1 O ASP E 7 N HIS A 6 SHEET 5 AA1 6 ALA F 2 VAL F 12 1 O ASP F 7 N HIS E 6 SHEET 6 AA1 6 ALA G 2 VAL G 12 1 O ASP G 7 N HIS F 6 SHEET 1 AA2 6 GLN D 15 PHE D 19 0 SHEET 2 AA2 6 GLN C 15 PHE C 19 1 N LEU C 17 O LYS D 16 SHEET 3 AA2 6 GLN A 15 PHE A 19 1 N LEU A 17 O LYS C 16 SHEET 4 AA2 6 GLN E 15 PHE E 19 1 O LEU E 17 N LYS A 16 SHEET 5 AA2 6 GLN F 15 PHE F 19 1 O LEU F 17 N LYS E 16 SHEET 6 AA2 6 GLN G 15 PHE G 19 1 O LEU G 17 N LYS F 16 SHEET 1 AA3 6 GLY D 33 LEU D 34 0 SHEET 2 AA3 6 GLY C 33 LEU C 34 1 N GLY C 33 O LEU D 34 SHEET 3 AA3 6 GLY A 33 LEU A 34 1 N GLY A 33 O LEU C 34 SHEET 4 AA3 6 GLY E 33 LEU E 34 1 O GLY E 33 N LEU A 34 SHEET 5 AA3 6 GLY F 33 LEU F 34 1 O GLY F 33 N LEU E 34 SHEET 6 AA3 6 GLY G 33 LEU G 34 1 O GLY G 33 N LEU F 34 SHEET 1 AA4 6 GLU I 3 VAL I 12 0 SHEET 2 AA4 6 GLU H 3 VAL H 12 1 N GLU H 3 O PHE I 4 SHEET 3 AA4 6 GLU B 3 VAL B 12 1 N GLU B 3 O PHE H 4 SHEET 4 AA4 6 GLU J 3 VAL J 12 1 O GLU J 3 N PHE B 4 SHEET 5 AA4 6 GLU K 3 VAL K 12 1 O GLU K 3 N PHE J 4 SHEET 6 AA4 6 GLU L 3 VAL L 12 1 O GLU L 3 N PHE K 4 SHEET 1 AA5 6 GLN I 15 PHE I 19 0 SHEET 2 AA5 6 GLN H 15 PHE H 19 1 N LEU H 17 O LYS I 16 SHEET 3 AA5 6 GLN B 15 PHE B 19 1 N LEU B 17 O LYS H 16 SHEET 4 AA5 6 GLN J 15 PHE J 19 1 O LEU J 17 N LYS B 16 SHEET 5 AA5 6 GLN K 15 PHE K 19 1 O LEU K 17 N LYS J 16 SHEET 6 AA5 6 GLN L 15 PHE L 19 1 O LEU L 17 N LYS K 16 SHEET 1 AA6 6 GLY I 33 LEU I 34 0 SHEET 2 AA6 6 GLY H 33 LEU H 34 1 N GLY H 33 O LEU I 34 SHEET 3 AA6 6 GLY B 33 LEU B 34 1 N GLY B 33 O LEU H 34 SHEET 4 AA6 6 GLY J 33 LEU J 34 1 O GLY J 33 N LEU B 34 SHEET 5 AA6 6 GLY K 33 LEU K 34 1 O GLY K 33 N LEU J 34 SHEET 6 AA6 6 GLY L 33 LEU L 34 1 O GLY L 33 N LEU K 34 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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