HEADER PROTEIN FIBRIL 15-JUL-25 9RZF TITLE STRUCTURE OF IN-VIVO FORMED ALPHA-SYNUCLEIN FIBRILS PURIFIED FROM A TITLE 2 M83+/- MOUSE BRAIN INJECTED WITH RECOMBINANT 1B FIBRILS 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; COMPND 8 OTHER_DETAILS: THE FIBRIL WAS PURIFIED FROM A MOUSE, THIS MOUSE MODEL COMPND 9 EXPRESSES A HUMANISED VERSION OF THE ALPHA-SYNUCLEIN PROTEIN. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: HEMIZYGOUS A53T ALPHA-SYNUCLEIN TRANSGENIC LINE M83; SOURCE 6 ORGAN: BRAIN; SOURCE 7 GENE: SNCA, NACP, PARK1; SOURCE 8 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 9 EXPRESSION_SYSTEM_COMMON: HOUSE MOUSE; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM_STRAIN: HEMIZYGOUS A53T ALPHA-SYNUCLEIN TRANSGENIC SOURCE 12 LINE M83 KEYWDS ALPHA-SYNUCLEIN, PRION-LIKE, FIBRIL, PAIRED HELICAL FILAMENT, PROTEIN KEYWDS 2 FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR L.VAN DEN HEUVEL,D.BURGER,M.KASHYRINA,H.DE LA SEIGLIERE,A.J.LEWIS, AUTHOR 2 F.DE NUCCIO,I.MOHAMMED,J.VERCHERE,C.FEUILLIE,M.BERBON,M.AROTCARENA, AUTHOR 3 A.RETAILLEAU,E.BEZARD,M.CANRON,W.G.MEISSNER,A.LOQUET,L.BOUSSET, AUTHOR 4 C.POUJOL,K.P.R.NILSSON,F.LAFERRIERE,T.BARON,D.D.LOFRUMENTO,F.DE AUTHOR 5 GIORGI,H.STAHLBERG,F.ICHAS REVDAT 6 24-DEC-25 9RZF 1 JRNL REVDAT 5 19-NOV-25 9RZF 1 JRNL REVDAT 4 05-NOV-25 9RZF 1 JRNL REVDAT 3 24-SEP-25 9RZF 1 COMPND SOURCE JRNL REVDAT 2 13-AUG-25 9RZF 1 DBREF SEQADV REVDAT 1 30-JUL-25 9RZF 0 JRNL AUTH D.BURGER,M.KASHYRINA,L.VAN DEN HEUVEL,H.DE LA SEIGLIERE, JRNL AUTH 2 A.J.LEWIS,F.DE NUCCIO,I.MOHAMMED,J.VERCHERE,C.FEUILLIE, JRNL AUTH 3 M.BERBON,M.L.AROTCARENA,A.RETAILLEAU,E.BEZARD,M.H.CANRON, JRNL AUTH 4 W.G.MEISSNER,A.LOQUET,L.BOUSSET,C.POUJOL,K.P.R.NILSSON, JRNL AUTH 5 F.LAFERRIERE,T.BARON,D.D.LOFRUMENTO,F.DE GIORGI,H.STAHLBERG, JRNL AUTH 6 F.ICHAS JRNL TITL SYNTHETIC ALPHA-SYNUCLEIN FIBRILS REPLICATE IN MICE CAUSING JRNL TITL 2 MSA-LIKE PATHOLOGY. JRNL REF NATURE V. 648 409 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 41193804 JRNL DOI 10.1038/S41586-025-09698-1 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, CRYOSPARC, EPU, CTFFIND, COOT, REMARK 3 UCSF CHIMERAX, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9EUU REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : A RIGID-BODY FIT WAS DONE USING CHIMERAX AND A REMARK 3 SUBSEQUENT JIGGLE FIT AND ALL-ATOM REFINEMENT WAS DONE IN COOT. 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 1913 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 9RZF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1292149325. 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 FIBRIL PURIFIED REMARK 245 FROM THE BRAIN OF A 1B-INJECTED REMARK 245 M83+/- MOUSE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : THE GRIDS WERE NOT GLOW REMARK 245 -DISCHARGED REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 42812 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 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) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA 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 LYS A 43 51.25 -119.24 REMARK 500 GLU E 46 -156.29 -84.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9EUU RELATED DB: PDB REMARK 900 9EUU IS THE STRUCTURE OF THE RECOMBINANT 1B FIBRIL SEEDS USED TO REMARK 900 INDUCE PATHOLOGY IN THE M83+/- MOUSE. REMARK 900 RELATED ID: EMD-54402 RELATED DB: EMDB REMARK 900 STRUCTURE OF IN-VIVO FORMED ALPHA-SYNUCLEIN FIBRILS PURIFIED FROM A REMARK 900 M83+/- MOUSE BRAIN INJECTED WITH RECOMBINANT 1B FIBRILS DBREF 9RZF A 37 97 UNP P37840 SYUA_HUMAN 37 97 DBREF 9RZF B 37 97 UNP P37840 SYUA_HUMAN 37 97 DBREF 9RZF C 37 97 UNP P37840 SYUA_HUMAN 37 97 DBREF 9RZF D 37 97 UNP P37840 SYUA_HUMAN 37 97 DBREF 9RZF E 37 97 UNP P37840 SYUA_HUMAN 37 97 DBREF 9RZF F 37 97 UNP P37840 SYUA_HUMAN 37 97 SEQADV 9RZF THR A 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQADV 9RZF THR B 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQADV 9RZF THR C 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQADV 9RZF THR D 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQADV 9RZF THR E 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQADV 9RZF THR F 53 UNP P37840 ALA 53 ENGINEERED MUTATION SEQRES 1 A 61 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 A 61 HIS GLY VAL THR THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 A 61 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 A 61 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 A 61 ALA ALA ALA THR GLY PHE VAL LYS LYS SEQRES 1 B 61 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 B 61 HIS GLY VAL THR THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 B 61 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 B 61 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 B 61 ALA ALA ALA THR GLY PHE VAL LYS LYS SEQRES 1 C 61 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 C 61 HIS GLY VAL THR THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 C 61 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 C 61 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 C 61 ALA ALA ALA THR GLY PHE VAL LYS LYS SEQRES 1 D 61 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 D 61 HIS GLY VAL THR THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 D 61 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 D 61 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 D 61 ALA ALA ALA THR GLY PHE VAL LYS LYS SEQRES 1 E 61 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 E 61 HIS GLY VAL THR THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 E 61 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 E 61 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 E 61 ALA ALA ALA THR GLY PHE VAL LYS LYS SEQRES 1 F 61 VAL LEU TYR VAL GLY SER LYS THR LYS GLU GLY VAL VAL SEQRES 2 F 61 HIS GLY VAL THR THR VAL ALA GLU LYS THR LYS GLU GLN SEQRES 3 F 61 VAL THR ASN VAL GLY GLY ALA VAL VAL THR GLY VAL THR SEQRES 4 F 61 ALA VAL ALA GLN LYS THR VAL GLU GLY ALA GLY SER ILE SEQRES 5 F 61 ALA ALA ALA THR GLY PHE VAL LYS LYS SHEET 1 AA1 3 LEU C 38 VAL C 40 0 SHEET 2 AA1 3 LEU A 38 VAL A 40 1 N VAL A 40 O TYR C 39 SHEET 3 AA1 3 LEU E 38 VAL E 40 1 O VAL E 40 N TYR A 39 SHEET 1 AA2 2 LYS A 45 GLU A 46 0 SHEET 2 AA2 2 LYS C 45 GLU C 46 1 O GLU C 46 N LYS A 45 SHEET 1 AA3 3 VAL C 49 VAL C 55 0 SHEET 2 AA3 3 VAL A 49 VAL A 55 1 N VAL A 55 O THR C 54 SHEET 3 AA3 3 VAL E 49 VAL E 55 1 O VAL E 55 N THR A 54 SHEET 1 AA4 3 LYS C 58 GLU C 61 0 SHEET 2 AA4 3 LYS A 58 GLU A 61 1 N LYS A 60 O THR C 59 SHEET 3 AA4 3 LYS E 58 GLU E 61 1 O LYS E 60 N GLU A 61 SHEET 1 AA5 3 ALA C 69 ALA C 78 0 SHEET 2 AA5 3 ALA A 69 ALA A 78 1 N VAL A 77 O ALA C 76 SHEET 3 AA5 3 ALA E 69 ALA E 78 1 O VAL E 77 N ALA A 76 SHEET 1 AA6 3 THR C 81 GLU C 83 0 SHEET 2 AA6 3 THR A 81 GLU A 83 1 N VAL A 82 O GLU C 83 SHEET 3 AA6 3 THR E 81 VAL E 82 1 O VAL E 82 N GLU A 83 SHEET 1 AA7 3 ILE C 88 LYS C 96 0 SHEET 2 AA7 3 ILE A 88 LYS A 96 1 N ALA A 89 O ILE C 88 SHEET 3 AA7 3 ILE E 88 LYS E 96 1 O ALA E 89 N ILE A 88 SHEET 1 AA8 2 LEU B 38 TYR B 39 0 SHEET 2 AA8 2 LEU D 38 TYR D 39 1 O TYR D 39 N LEU B 38 SHEET 1 AA9 3 THR D 44 GLU D 46 0 SHEET 2 AA9 3 LYS B 43 GLU B 46 1 N LYS B 45 O GLU D 46 SHEET 3 AA9 3 LYS F 43 GLU F 46 1 O LYS F 45 N GLU B 46 SHEET 1 AB1 3 VAL D 49 HIS D 50 0 SHEET 2 AB1 3 VAL B 49 HIS B 50 1 N HIS B 50 O VAL D 49 SHEET 3 AB1 3 VAL F 49 HIS F 50 1 O HIS F 50 N VAL B 49 SHEET 1 AB2 3 THR D 54 VAL D 55 0 SHEET 2 AB2 3 THR B 54 VAL B 55 1 N VAL B 55 O THR D 54 SHEET 3 AB2 3 THR F 54 VAL F 55 1 O VAL F 55 N THR B 54 SHEET 1 AB3 3 THR D 59 GLU D 61 0 SHEET 2 AB3 3 LYS B 58 GLU B 61 1 N LYS B 60 O GLU D 61 SHEET 3 AB3 3 LYS F 58 GLU F 61 1 O LYS F 60 N GLU B 61 SHEET 1 AB4 3 ALA D 69 VAL D 71 0 SHEET 2 AB4 3 ALA B 69 VAL B 71 1 N ALA B 69 O VAL D 70 SHEET 3 AB4 3 ALA F 69 VAL F 71 1 O VAL F 71 N VAL B 70 SHEET 1 AB5 3 VAL D 74 ALA D 78 0 SHEET 2 AB5 3 VAL B 74 ALA B 78 1 N VAL B 77 O ALA D 76 SHEET 3 AB5 3 VAL F 74 ALA F 78 1 O VAL F 77 N ALA B 76 SHEET 1 AB6 2 THR B 81 VAL B 82 0 SHEET 2 AB6 2 THR F 81 VAL F 82 1 O VAL F 82 N THR B 81 SHEET 1 AB7 3 ILE D 88 LYS D 96 0 SHEET 2 AB7 3 ILE B 88 LYS B 96 1 N ALA B 90 O ALA D 91 SHEET 3 AB7 3 ILE F 88 LYS F 96 1 O ALA F 90 N ALA B 91 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 MASTER 127 0 0 0 45 0 0 6 2538 6 0 30 END