HEADER PROTEIN FIBRIL 27-JUN-18 6A6B TITLE CRYO-EM STRUCTURE OF ALPHA-SYNUCLEIN FIBER COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-SYNUCLEIN; COMPND 3 CHAIN: A, B, C, D, E, F, G, H, I, J, K, L; COMPND 4 FRAGMENT: UNP RESIDUES 37-99; COMPND 5 SYNONYM: NON-A BETA COMPONENT OF AD AMYLOID,NON-A4 COMPONENT OF COMPND 6 AMYLOID PRECURSOR,NACP; 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: SNCA, NACP, PARK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS ALPHA-SYN FIBER, PARKINSON DISEASE, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.W.LI,C.Y.ZHAO,F.LUO,Z.LIU,X.GUI,Z.LUO,X.ZHANG,D.LI,C.LIU,X.LI REVDAT 4 27-MAR-24 6A6B 1 REMARK REVDAT 3 24-OCT-18 6A6B 1 JRNL REVDAT 2 01-AUG-18 6A6B 1 REMARK REVDAT 1 11-JUL-18 6A6B 0 JRNL AUTH Y.LI,C.ZHAO,F.LUO,Z.LIU,X.GUI,Z.LUO,X.ZHANG,D.LI,C.LIU,X.LI JRNL TITL AMYLOID FIBRIL STRUCTURE OF ALPHA-SYNUCLEIN DETERMINED BY JRNL TITL 2 CRYO-ELECTRON MICROSCOPY JRNL REF CELL RES. V. 28 897 2018 JRNL REFN ISSN 1748-7838 JRNL PMID 30065316 JRNL DOI 10.1038/S41422-018-0075-X REMARK 2 REMARK 2 RESOLUTION. 3.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND, RELION 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) : 3.070 REMARK 3 NUMBER OF PARTICLES : 43677 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 6A6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008227. 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 : ALPHA-SYNUCLEIN FIBER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : 4 MICROL OF ALPHA-SYN FIBRIL REMARK 245 SOLUTION WAS APPLIED TO A GLOW- REMARK 245 DISCHARGED HOLEY CARBON GRID REMARK 245 (QUANTIFOIL R1.2/1.3, 300 MESH), REMARK 245 BLOTTED FOR 6 S, AND PLUNGE- REMARK 245 FROZEN IN LIQUID ETHANE USING REMARK 245 FEI VITROBOT MARK IV. 95% REMARK 245 HUMIDITY, 16 DEGREES REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 SUMMIT (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 : 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J, REMARK 350 AND CHAINS: K, 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6988 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ALPHA-SYNUCLEIN FIBER DBREF 6A6B A 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B B 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B C 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B D 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B E 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B F 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B G 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B H 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B I 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B J 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B K 37 99 UNP P37840 SYUA_HUMAN 37 99 DBREF 6A6B L 37 99 UNP P37840 SYUA_HUMAN 37 99 SEQRES 1 A 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 A 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 A 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 A 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 A 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 B 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 B 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 B 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 B 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 B 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 C 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 C 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 C 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 C 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 C 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 D 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 D 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 D 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 D 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 D 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 E 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 E 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 E 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 E 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 E 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 F 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 F 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 F 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 F 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 F 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 G 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 G 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 G 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 G 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 G 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 H 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 H 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 H 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 H 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 H 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 I 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 I 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 I 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 I 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 I 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 J 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 J 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 J 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 J 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 J 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 K 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 K 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 K 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 K 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 K 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SEQRES 1 L 63 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 L 63 HIS GLY VAL ALA THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 L 63 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 L 63 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 L 63 ALA ALA ALA THR GLY PHE VAL LYS LYS ASP GLN SHEET 1 AA1 6 VAL A 49 LYS A 58 0 SHEET 2 AA1 6 VAL B 49 LYS B 58 1 O LYS B 58 N GLU A 57 SHEET 3 AA1 6 VAL C 49 LYS C 58 1 O LYS C 58 N GLU B 57 SHEET 4 AA1 6 VAL D 49 LYS D 58 1 O VAL D 52 N ALA C 53 SHEET 5 AA1 6 VAL E 49 LYS E 58 1 O VAL E 52 N ALA D 53 SHEET 6 AA1 6 VAL F 49 LYS F 58 1 O LYS F 58 N GLU E 57 SHEET 1 AA2 6 GLU A 61 VAL A 63 0 SHEET 2 AA2 6 GLU B 61 VAL B 63 1 O VAL B 63 N GLN A 62 SHEET 3 AA2 6 GLU C 61 VAL C 63 1 O VAL C 63 N GLN B 62 SHEET 4 AA2 6 GLU D 61 VAL D 63 1 O VAL D 63 N GLN C 62 SHEET 5 AA2 6 GLU E 61 VAL E 63 1 O VAL E 63 N GLN D 62 SHEET 6 AA2 6 GLU F 61 VAL F 63 1 O VAL F 63 N GLN E 62 SHEET 1 AA3 6 VAL A 71 THR A 72 0 SHEET 2 AA3 6 VAL B 71 THR B 72 1 O THR B 72 N VAL A 71 SHEET 3 AA3 6 VAL C 71 THR C 72 1 O THR C 72 N VAL B 71 SHEET 4 AA3 6 VAL D 71 THR D 72 1 O THR D 72 N VAL C 71 SHEET 5 AA3 6 VAL E 71 THR E 72 1 O THR E 72 N VAL D 71 SHEET 6 AA3 6 VAL F 71 THR F 72 1 O THR F 72 N VAL E 71 SHEET 1 AA4 6 LYS A 80 VAL A 82 0 SHEET 2 AA4 6 LYS B 80 VAL B 82 1 O VAL B 82 N THR A 81 SHEET 3 AA4 6 LYS C 80 VAL C 82 1 O VAL C 82 N THR B 81 SHEET 4 AA4 6 LYS D 80 VAL D 82 1 O VAL D 82 N THR C 81 SHEET 5 AA4 6 LYS E 80 VAL E 82 1 O VAL E 82 N THR D 81 SHEET 6 AA4 6 LYS F 80 VAL F 82 1 O VAL F 82 N THR E 81 SHEET 1 AA5 6 ALA A 89 THR A 92 0 SHEET 2 AA5 6 ALA B 89 THR B 92 1 O THR B 92 N ALA A 91 SHEET 3 AA5 6 ALA C 89 THR C 92 1 O THR C 92 N ALA B 91 SHEET 4 AA5 6 ALA D 89 THR D 92 1 O THR D 92 N ALA C 91 SHEET 5 AA5 6 ALA E 89 THR E 92 1 O THR E 92 N ALA D 91 SHEET 6 AA5 6 ALA F 89 THR F 92 1 O THR F 92 N ALA E 91 SHEET 1 AA6 6 VAL G 49 LYS G 58 0 SHEET 2 AA6 6 VAL H 49 LYS H 58 1 O GLU H 57 N LYS G 58 SHEET 3 AA6 6 VAL I 49 LYS I 58 1 O GLU I 57 N LYS H 58 SHEET 4 AA6 6 VAL J 49 LYS J 58 1 O GLU J 57 N LYS I 58 SHEET 5 AA6 6 VAL K 49 LYS K 58 1 O GLU K 57 N LYS J 58 SHEET 6 AA6 6 VAL L 49 LYS L 58 1 O ALA L 53 N VAL K 52 SHEET 1 AA7 6 GLU G 61 VAL G 63 0 SHEET 2 AA7 6 GLU H 61 VAL H 63 1 O GLN H 62 N VAL G 63 SHEET 3 AA7 6 GLU I 61 VAL I 63 1 O GLN I 62 N VAL H 63 SHEET 4 AA7 6 GLU J 61 VAL J 63 1 O GLN J 62 N VAL I 63 SHEET 5 AA7 6 GLU K 61 VAL K 63 1 O GLN K 62 N VAL J 63 SHEET 6 AA7 6 GLU L 61 VAL L 63 1 O GLN L 62 N VAL K 63 SHEET 1 AA8 6 VAL G 71 THR G 72 0 SHEET 2 AA8 6 VAL H 71 THR H 72 1 O VAL H 71 N THR G 72 SHEET 3 AA8 6 VAL I 71 THR I 72 1 O VAL I 71 N THR H 72 SHEET 4 AA8 6 VAL J 71 THR J 72 1 O VAL J 71 N THR I 72 SHEET 5 AA8 6 VAL K 71 THR K 72 1 O VAL K 71 N THR J 72 SHEET 6 AA8 6 VAL L 71 THR L 72 1 O VAL L 71 N THR K 72 SHEET 1 AA9 6 LYS G 80 VAL G 82 0 SHEET 2 AA9 6 LYS H 80 VAL H 82 1 O THR H 81 N VAL G 82 SHEET 3 AA9 6 LYS I 80 VAL I 82 1 O THR I 81 N VAL H 82 SHEET 4 AA9 6 LYS J 80 VAL J 82 1 O THR J 81 N VAL I 82 SHEET 5 AA9 6 LYS K 80 VAL K 82 1 O THR K 81 N VAL J 82 SHEET 6 AA9 6 LYS L 80 VAL L 82 1 O THR L 81 N VAL K 82 SHEET 1 AB1 2 ALA G 89 THR G 92 0 SHEET 2 AB1 2 ALA H 89 THR H 92 1 O ALA H 91 N THR G 92 SHEET 1 AB2 3 ALA I 89 THR I 92 0 SHEET 2 AB2 3 ALA J 89 THR J 92 1 O ALA J 91 N THR I 92 SHEET 3 AB2 3 ALA K 89 THR K 92 1 O ALA K 91 N THR J 92 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