HEADER PROTEIN FIBRIL 14-AUG-17 5OQV TITLE NEAR-ATOMIC RESOLUTION FIBRIL STRUCTURE OF COMPLETE AMYLOID-BETA(1-42) TITLE 2 BY CRYO-EM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I; COMPND 4 SYNONYM: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 5 PRECURSOR PROTEIN,BETA-AMYLOID PRECURSOR PROTEIN,CEREBRAL VASCULAR COMPND 6 AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APP, A4, AD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLOID, FIBRIL, AGGREGATION, ALZHEIMER'S DISEASE, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR L.GREMER,D.SCHOELZEL,C.SCHENK,E.REINARTZ,J.LABAHN,R.RAVELLI,M.TUSCHE, AUTHOR 2 C.LOPEZ-IGLESIAS,W.HOYER,H.HEISE,D.WILLBOLD,G.F.SCHROEDER REVDAT 4 18-OCT-17 5OQV 1 JRNL REVDAT 3 27-SEP-17 5OQV 1 KEYWDS REVDAT 2 20-SEP-17 5OQV 1 JRNL REVDAT 1 13-SEP-17 5OQV 0 JRNL AUTH L.GREMER,D.SCHOLZEL,C.SCHENK,E.REINARTZ,J.LABAHN, JRNL AUTH 2 R.B.G.RAVELLI,M.TUSCHE,C.LOPEZ-IGLESIAS,W.HOYER,H.HEISE, JRNL AUTH 3 D.WILLBOLD,G.F.SCHRODER JRNL TITL FIBRIL STRUCTURE OF AMYLOID-BETA (1-42) BY CRYO-ELECTRON JRNL TITL 2 MICROSCOPY. JRNL REF SCIENCE V. 358 116 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 28882996 JRNL DOI 10.1126/SCIENCE.AAO2825 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, SPARX, SPARX, SPARX, SPARX, 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 : CROSS-CORRELATION COEFFICIENT 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) : 4.000 REMARK 3 NUMBER OF PARTICLES : 127765 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: FOR THE EVEN/ODD TEST, THE FIBRILS WERE SPLIT AFTER REMARK 3 THE FINAL RECONSTRUCTION (NO GOLD-STANDARD). THESE TWO HALF SETS REMARK 3 WERE THEN REFINED FURTHER INDEPENDENTLY FOR ANOTHER 12 REMARK 3 ITERATIONS. REMARK 4 REMARK 4 5OQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006213. 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 : BETA-AMYLOID PROTEIN 42 FIBRILS REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 2.5 MICROL SAMPLE WAS APPLIED REMARK 245 TO THE GRID, BLOTTED FOR 2.5 S REMARK 245 BEFORE PLUNGING. REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 2.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 2026 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI ARCTICA REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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) : 24.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 110000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: NONAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: NONAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -125.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I 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 ALA A 2 110.94 -160.42 REMARK 500 TYR A 10 78.56 54.83 REMARK 500 LEU A 34 74.55 59.77 REMARK 500 ALA B 2 110.95 -160.36 REMARK 500 TYR B 10 78.55 54.86 REMARK 500 LEU B 34 74.51 59.81 REMARK 500 ALA C 2 110.95 -160.37 REMARK 500 TYR C 10 78.56 54.86 REMARK 500 LEU C 34 74.51 59.79 REMARK 500 ALA D 2 110.96 -160.40 REMARK 500 TYR D 10 78.57 54.82 REMARK 500 LEU D 34 74.51 59.77 REMARK 500 ALA E 2 110.98 -160.37 REMARK 500 TYR E 10 78.59 54.76 REMARK 500 LEU E 34 74.49 59.71 REMARK 500 ALA F 2 110.93 -160.43 REMARK 500 TYR F 10 78.53 54.84 REMARK 500 LEU F 34 74.55 59.78 REMARK 500 ALA G 2 110.96 -160.40 REMARK 500 TYR G 10 78.52 54.86 REMARK 500 LEU G 34 74.54 59.70 REMARK 500 ALA H 2 111.01 -160.40 REMARK 500 TYR H 10 78.55 54.87 REMARK 500 LEU H 34 74.51 59.75 REMARK 500 ALA I 2 110.96 -160.41 REMARK 500 TYR I 10 78.54 54.82 REMARK 500 LEU I 34 74.55 59.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27212 RELATED DB: BMRB REMARK 900 THESE SOLID-STATE NMR DATA WERE COLLECTED ON THE SAME SAMPLE. REMARK 900 RELATED ID: EMD-3851 RELATED DB: EMDB REMARK 900 NEAR-ATOMIC RESOLUTION FIBRIL STRUCTURE OF COMPLETE AMYLOID-BETA(1- REMARK 900 42) BY CRYO-EM DBREF 5OQV A 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV B 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV C 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV D 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV E 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV F 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV G 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV H 1 42 UNP P05067 A4_HUMAN 672 713 DBREF 5OQV I 1 42 UNP P05067 A4_HUMAN 672 713 SEQRES 1 A 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 A 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 A 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 A 42 VAL ILE ALA SEQRES 1 B 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 B 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 B 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 B 42 VAL ILE ALA SEQRES 1 C 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 C 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 C 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 C 42 VAL ILE ALA SEQRES 1 D 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 D 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 D 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 D 42 VAL ILE ALA SEQRES 1 E 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 E 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 E 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 E 42 VAL ILE ALA SEQRES 1 F 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 F 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 F 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 F 42 VAL ILE ALA SEQRES 1 G 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 G 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 G 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 G 42 VAL ILE ALA SEQRES 1 H 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 H 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 H 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 H 42 VAL ILE ALA SEQRES 1 I 42 ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS SEQRES 2 I 42 HIS GLN LYS LEU VAL PHE PHE ALA GLU ASP VAL GLY SER SEQRES 3 I 42 ASN LYS GLY ALA ILE ILE GLY LEU MET VAL GLY GLY VAL SEQRES 4 I 42 VAL ILE ALA SHEET 1 AA1 5 GLU E 3 GLU E 22 0 SHEET 2 AA1 5 GLU C 3 GLU C 22 1 N PHE C 4 O ARG E 5 SHEET 3 AA1 5 GLU A 3 GLU A 22 1 N PHE A 4 O ARG C 5 SHEET 4 AA1 5 GLU H 3 GLU H 22 1 O PHE H 4 N ARG A 5 SHEET 5 AA1 5 GLU F 3 GLU F 22 1 N PHE F 4 O ARG H 5 SHEET 1 AA2 5 LYS E 28 MET E 35 0 SHEET 2 AA2 5 LYS C 28 MET C 35 1 N ILE C 31 O ALA E 30 SHEET 3 AA2 5 LYS A 28 MET A 35 1 N ILE A 31 O ALA C 30 SHEET 4 AA2 5 LYS H 28 MET H 35 1 O ILE H 31 N ALA A 30 SHEET 5 AA2 5 LYS F 28 MET F 35 1 N ILE F 31 O ALA H 30 SHEET 1 AA3 5 VAL E 40 ILE E 41 0 SHEET 2 AA3 5 VAL C 40 ILE C 41 1 N ILE C 41 O VAL E 40 SHEET 3 AA3 5 VAL A 40 ILE A 41 1 N ILE A 41 O VAL C 40 SHEET 4 AA3 5 VAL H 40 ILE H 41 1 O ILE H 41 N VAL A 40 SHEET 5 AA3 5 VAL F 40 ILE F 41 1 N ILE F 41 O VAL H 40 SHEET 1 AA4 4 GLU D 3 GLU D 22 0 SHEET 2 AA4 4 GLU B 3 GLU B 22 1 N PHE B 4 O ARG D 5 SHEET 3 AA4 4 GLU I 3 GLU I 22 1 O PHE I 4 N ARG B 5 SHEET 4 AA4 4 GLU G 3 GLU G 22 1 N PHE G 4 O ARG I 5 SHEET 1 AA5 4 LYS D 28 MET D 35 0 SHEET 2 AA5 4 LYS B 28 MET B 35 1 N ILE B 31 O ALA D 30 SHEET 3 AA5 4 LYS I 28 MET I 35 1 O ILE I 31 N ALA B 30 SHEET 4 AA5 4 LYS G 28 MET G 35 1 N ILE G 31 O ALA I 30 SHEET 1 AA6 4 VAL D 40 ILE D 41 0 SHEET 2 AA6 4 VAL B 40 ILE B 41 1 N ILE B 41 O VAL D 40 SHEET 3 AA6 4 VAL I 40 ILE I 41 1 O ILE I 41 N VAL B 40 SHEET 4 AA6 4 VAL G 40 ILE G 41 1 N ILE G 41 O VAL I 40 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