HEADER PROTEIN FIBRIL 21-OCT-19 6L4S TITLE CRYO-EM STRUCTURE OF ALPHA-SYNUCLEIN FIBER MUTATION TYPE E46K COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-SYNUCLEIN; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: NON-A BETA COMPONENT OF AD AMYLOID,NON-A4 COMPONENT OF COMPND 5 AMYLOID PRECURSOR,NACP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12 KEYWDS ALPHA-SYN FIBER, PARKINSON DISEASE, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Y.W.LI,K.ZHAO,C.LIU,X.LI REVDAT 2 10-NOV-21 6L4S 1 JRNL REVDAT 1 29-APR-20 6L4S 0 JRNL AUTH K.ZHAO,Y.LI,Z.LIU,H.LONG,C.ZHAO,F.LUO,Y.SUN,Y.TAO,X.D.SU, JRNL AUTH 2 D.LI,X.LI,C.LIU JRNL TITL PARKINSON'S DISEASE ASSOCIATED MUTATION E46K OF JRNL TITL 2 ALPHA-SYNUCLEIN TRIGGERS THE FORMATION OF A DISTINCT FIBRIL JRNL TITL 3 STRUCTURE. JRNL REF NAT COMMUN V. 11 2643 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32457390 JRNL DOI 10.1038/S41467-020-16386-3 REMARK 2 REMARK 2 RESOLUTION. 3.37 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND, RELION, 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) : 3.370 REMARK 3 NUMBER OF PARTICLES : 18009 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 6L4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300013835. 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 MUTATION REMARK 245 TYPE E46K 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 : 7.50 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 THR A 92 -61.72 -96.77 REMARK 500 THR B 92 -61.69 -96.74 REMARK 500 THR C 92 -61.68 -96.71 REMARK 500 THR D 92 -61.68 -96.77 REMARK 500 THR E 92 -61.73 -96.76 REMARK 500 THR F 92 -61.72 -96.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-0833 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ALPHA-SYNUCLEIN FIBER MUTATION TYPE E46K DBREF 6L4S A 45 99 UNP P37840 SYUA_HUMAN 45 99 DBREF 6L4S B 45 99 UNP P37840 SYUA_HUMAN 45 99 DBREF 6L4S C 45 99 UNP P37840 SYUA_HUMAN 45 99 DBREF 6L4S D 45 99 UNP P37840 SYUA_HUMAN 45 99 DBREF 6L4S E 45 99 UNP P37840 SYUA_HUMAN 45 99 DBREF 6L4S F 45 99 UNP P37840 SYUA_HUMAN 45 99 SEQADV 6L4S LYS A 46 UNP P37840 GLU 46 ENGINEERED MUTATION SEQADV 6L4S LYS B 46 UNP P37840 GLU 46 ENGINEERED MUTATION SEQADV 6L4S LYS C 46 UNP P37840 GLU 46 ENGINEERED MUTATION SEQADV 6L4S LYS D 46 UNP P37840 GLU 46 ENGINEERED MUTATION SEQADV 6L4S LYS E 46 UNP P37840 GLU 46 ENGINEERED MUTATION SEQADV 6L4S LYS F 46 UNP P37840 GLU 46 ENGINEERED MUTATION SEQRES 1 A 55 LYS LYS GLY VAL VAL HIS GLY VAL ALA THR VAL ALA GLU SEQRES 2 A 55 LYS THR LYS GLU GLN VAL THR ASN VAL GLY GLY ALA VAL SEQRES 3 A 55 VAL THR GLY VAL THR ALA VAL ALA GLN LYS THR VAL GLU SEQRES 4 A 55 GLY ALA GLY SER ILE ALA ALA ALA THR GLY PHE VAL LYS SEQRES 5 A 55 LYS ASP GLN SEQRES 1 B 55 LYS LYS GLY VAL VAL HIS GLY VAL ALA THR VAL ALA GLU SEQRES 2 B 55 LYS THR LYS GLU GLN VAL THR ASN VAL GLY GLY ALA VAL SEQRES 3 B 55 VAL THR GLY VAL THR ALA VAL ALA GLN LYS THR VAL GLU SEQRES 4 B 55 GLY ALA GLY SER ILE ALA ALA ALA THR GLY PHE VAL LYS SEQRES 5 B 55 LYS ASP GLN SEQRES 1 C 55 LYS LYS GLY VAL VAL HIS GLY VAL ALA THR VAL ALA GLU SEQRES 2 C 55 LYS THR LYS GLU GLN VAL THR ASN VAL GLY GLY ALA VAL SEQRES 3 C 55 VAL THR GLY VAL THR ALA VAL ALA GLN LYS THR VAL GLU SEQRES 4 C 55 GLY ALA GLY SER ILE ALA ALA ALA THR GLY PHE VAL LYS SEQRES 5 C 55 LYS ASP GLN SEQRES 1 D 55 LYS LYS GLY VAL VAL HIS GLY VAL ALA THR VAL ALA GLU SEQRES 2 D 55 LYS THR LYS GLU GLN VAL THR ASN VAL GLY GLY ALA VAL SEQRES 3 D 55 VAL THR GLY VAL THR ALA VAL ALA GLN LYS THR VAL GLU SEQRES 4 D 55 GLY ALA GLY SER ILE ALA ALA ALA THR GLY PHE VAL LYS SEQRES 5 D 55 LYS ASP GLN SEQRES 1 E 55 LYS LYS GLY VAL VAL HIS GLY VAL ALA THR VAL ALA GLU SEQRES 2 E 55 LYS THR LYS GLU GLN VAL THR ASN VAL GLY GLY ALA VAL SEQRES 3 E 55 VAL THR GLY VAL THR ALA VAL ALA GLN LYS THR VAL GLU SEQRES 4 E 55 GLY ALA GLY SER ILE ALA ALA ALA THR GLY PHE VAL LYS SEQRES 5 E 55 LYS ASP GLN SEQRES 1 F 55 LYS LYS GLY VAL VAL HIS GLY VAL ALA THR VAL ALA GLU SEQRES 2 F 55 LYS THR LYS GLU GLN VAL THR ASN VAL GLY GLY ALA VAL SEQRES 3 F 55 VAL THR GLY VAL THR ALA VAL ALA GLN LYS THR VAL GLU SEQRES 4 F 55 GLY ALA GLY SER ILE ALA ALA ALA THR GLY PHE VAL LYS SEQRES 5 F 55 LYS ASP GLN SHEET 1 AA1 3 LYS C 46 VAL C 48 0 SHEET 2 AA1 3 LYS A 46 VAL A 48 1 N VAL A 48 O GLY C 47 SHEET 3 AA1 3 LYS E 46 VAL E 48 1 O VAL E 48 N GLY A 47 SHEET 1 AA2 3 VAL C 63 THR C 64 0 SHEET 2 AA2 3 GLU A 61 THR A 64 1 N THR A 64 O VAL C 63 SHEET 3 AA2 3 GLU E 61 THR E 64 1 O THR E 64 N VAL A 63 SHEET 1 AA3 3 ALA C 69 VAL C 71 0 SHEET 2 AA3 3 ALA A 69 VAL A 71 1 N VAL A 71 O VAL C 70 SHEET 3 AA3 3 ALA E 69 VAL E 71 1 O VAL E 71 N VAL A 70 SHEET 1 AA4 3 THR C 75 ALA C 78 0 SHEET 2 AA4 3 THR A 75 ALA A 78 1 N VAL A 77 O ALA C 76 SHEET 3 AA4 3 THR E 75 ALA E 78 1 O VAL E 77 N ALA A 76 SHEET 1 AA5 3 ALA C 91 GLY C 93 0 SHEET 2 AA5 3 ALA A 91 GLY A 93 1 N GLY A 93 O THR C 92 SHEET 3 AA5 3 ALA E 91 GLY E 93 1 O GLY E 93 N THR A 92 SHEET 1 AA6 3 LYS D 46 VAL D 48 0 SHEET 2 AA6 3 LYS B 46 VAL B 48 1 N VAL B 48 O GLY D 47 SHEET 3 AA6 3 LYS F 46 VAL F 48 1 O VAL F 48 N GLY B 47 SHEET 1 AA7 3 VAL D 63 THR D 64 0 SHEET 2 AA7 3 VAL B 63 THR B 64 1 N THR B 64 O VAL D 63 SHEET 3 AA7 3 VAL F 63 THR F 64 1 O THR F 64 N VAL B 63 SHEET 1 AA8 3 ALA D 69 VAL D 71 0 SHEET 2 AA8 3 ALA B 69 VAL B 71 1 N VAL B 71 O VAL D 70 SHEET 3 AA8 3 ALA F 69 VAL F 71 1 O VAL F 71 N VAL B 70 SHEET 1 AA9 3 THR D 75 ALA D 78 0 SHEET 2 AA9 3 THR B 75 ALA B 78 1 N VAL B 77 O ALA D 78 SHEET 3 AA9 3 THR F 75 ALA F 78 1 O VAL F 77 N ALA B 78 SHEET 1 AB1 3 ALA D 91 GLY D 93 0 SHEET 2 AB1 3 ALA B 91 GLY B 93 1 N GLY B 93 O THR D 92 SHEET 3 AB1 3 ALA F 91 GLY F 93 1 O GLY F 93 N THR B 92 CISPEP 1 GLY A 51 VAL A 52 0 10.48 CISPEP 2 GLY A 67 GLY A 68 0 1.17 CISPEP 3 ALA A 85 GLY A 86 0 2.60 CISPEP 4 GLY B 51 VAL B 52 0 10.49 CISPEP 5 GLY B 67 GLY B 68 0 1.16 CISPEP 6 ALA B 85 GLY B 86 0 2.62 CISPEP 7 GLY C 51 VAL C 52 0 10.60 CISPEP 8 GLY C 67 GLY C 68 0 1.21 CISPEP 9 ALA C 85 GLY C 86 0 2.74 CISPEP 10 GLY D 51 VAL D 52 0 10.60 CISPEP 11 GLY D 67 GLY D 68 0 1.17 CISPEP 12 ALA D 85 GLY D 86 0 2.66 CISPEP 13 GLY E 51 VAL E 52 0 10.53 CISPEP 14 GLY E 67 GLY E 68 0 1.21 CISPEP 15 ALA E 85 GLY E 86 0 2.66 CISPEP 16 GLY F 51 VAL F 52 0 10.39 CISPEP 17 GLY F 67 GLY F 68 0 1.18 CISPEP 18 ALA F 85 GLY F 86 0 2.65 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