HEADER PROTEIN FIBRIL 26-MAY-22 8A00 TITLE INFECTIOUS MOUSE-ADAPTED ME7 SCRAPIE PRION FIBRIL PURIFIED FROM TITLE 2 TERMINALLY-INFECTED MOUSE BRAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A, C, B; COMPND 4 SYNONYM: PRP,PRP27-30,PRP33-35C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090 KEYWDS PRION, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR S.W.MANKA,A.WENBORN,J.BETTS,S.JOINER,H.R.SAIBIL,J.COLLINGE, AUTHOR 2 J.D.F.WADSWORTH REVDAT 3 10-MAY-23 8A00 1 JRNL REVDAT 2 08-FEB-23 8A00 1 JRNL REVDAT 1 18-JAN-23 8A00 0 JRNL AUTH S.W.MANKA,A.WENBORN,J.BETTS,S.JOINER,H.R.SAIBIL,J.COLLINGE, JRNL AUTH 2 J.D.F.WADSWORTH JRNL TITL A STRUCTURAL BASIS FOR PRION STRAIN DIVERSITY. JRNL REF NAT.CHEM.BIOL. V. 19 607 2023 JRNL REFN ESSN 1552-4469 JRNL PMID 36646960 JRNL DOI 10.1038/S41589-022-01229-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.W.MANKA,A.WENBORN,J.BETTS,S.JOINER,H.R.SAIBIL,J.COLLINGE, REMARK 1 AUTH 2 J.D.F.WADSWORTH REMARK 1 TITL A STRUCTURAL BASIS FOR PRION STRAIN DIVERSITY REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.05.17.492259 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, COOT, RELION, RELION, RELION, REMARK 3 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 : FLEXIBLE FIT 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) : 2.600 REMARK 3 NUMBER OF PARTICLES : 40239 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 8A00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1292123282. 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 : AMYLOID FIBRIL OF PRION PROTEIN 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 : 6.80 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 K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 4900.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B 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 VAL A 165 -63.52 -97.84 REMARK 500 VAL A 214 70.47 61.19 REMARK 500 VAL C 165 -63.22 -106.11 REMARK 500 VAL C 214 70.32 58.79 REMARK 500 LYS C 219 -60.41 -95.34 REMARK 500 ASP B 146 141.72 -170.88 REMARK 500 VAL B 214 70.10 63.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-15043 RELATED DB: EMDB REMARK 900 INFECTIOUS MOUSE-ADAPTED ME7 SCRAPIE PRION FIBRIL PURIFIED FROM REMARK 900 TERMINALLY-INFECTED MOUSE BRAINS DBREF 8A00 A 94 229 UNP P04925 PRIO_MOUSE 94 229 DBREF 8A00 C 94 229 UNP P04925 PRIO_MOUSE 94 229 DBREF 8A00 B 94 229 UNP P04925 PRIO_MOUSE 94 229 SEQRES 1 A 136 THR HIS ASN GLN TRP ASN LYS PRO SER LYS PRO LYS THR SEQRES 2 A 136 ASN LEU LYS HIS VAL ALA GLY ALA ALA ALA ALA GLY ALA SEQRES 3 A 136 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA SEQRES 4 A 136 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU SEQRES 5 A 136 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN SEQRES 6 A 136 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN SEQRES 7 A 136 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS SEQRES 8 A 136 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE SEQRES 9 A 136 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU SEQRES 10 A 136 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA SEQRES 11 A 136 TYR TYR ASP GLY ARG ARG SEQRES 1 C 136 THR HIS ASN GLN TRP ASN LYS PRO SER LYS PRO LYS THR SEQRES 2 C 136 ASN LEU LYS HIS VAL ALA GLY ALA ALA ALA ALA GLY ALA SEQRES 3 C 136 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA SEQRES 4 C 136 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU SEQRES 5 C 136 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN SEQRES 6 C 136 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN SEQRES 7 C 136 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS SEQRES 8 C 136 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE SEQRES 9 C 136 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU SEQRES 10 C 136 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA SEQRES 11 C 136 TYR TYR ASP GLY ARG ARG SEQRES 1 B 136 THR HIS ASN GLN TRP ASN LYS PRO SER LYS PRO LYS THR SEQRES 2 B 136 ASN LEU LYS HIS VAL ALA GLY ALA ALA ALA ALA GLY ALA SEQRES 3 B 136 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA SEQRES 4 B 136 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU SEQRES 5 B 136 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN SEQRES 6 B 136 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN SEQRES 7 B 136 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS SEQRES 8 B 136 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE SEQRES 9 B 136 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU SEQRES 10 B 136 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA SEQRES 11 B 136 TYR TYR ASP GLY ARG ARG SHEET 1 AA1 3 HIS C 95 ASN C 99 0 SHEET 2 AA1 3 HIS A 95 ASN A 99 1 N TRP A 98 O GLN C 97 SHEET 3 AA1 3 HIS B 95 ASN B 99 1 O TRP B 98 N GLN A 97 SHEET 1 AA2 3 THR C 106 VAL C 111 0 SHEET 2 AA2 3 THR A 106 VAL A 111 1 N LYS A 109 O LEU C 108 SHEET 3 AA2 3 THR B 106 VAL B 111 1 O LYS B 109 N LEU A 108 SHEET 1 AA3 3 ALA C 114 ALA C 116 0 SHEET 2 AA3 3 ALA A 114 ALA A 116 1 N ALA A 115 O ALA C 116 SHEET 3 AA3 3 ALA B 114 ALA B 116 1 O ALA B 115 N ALA A 116 SHEET 1 AA4 3 ALA C 119 VAL C 121 0 SHEET 2 AA4 3 ALA A 119 VAL A 121 1 N VAL A 121 O VAL C 120 SHEET 3 AA4 3 ALA B 119 VAL B 121 1 O VAL B 121 N VAL A 120 SHEET 1 AA5 3 ALA C 132 SER C 134 0 SHEET 2 AA5 3 ALA A 132 SER A 134 1 N MET A 133 O ALA C 132 SHEET 3 AA5 3 ALA B 132 SER B 134 1 O MET B 133 N ALA A 132 SHEET 1 AA6 3 MET C 137 TRP C 144 0 SHEET 2 AA6 3 MET A 137 TRP A 144 1 N ASP A 143 O ASN C 142 SHEET 3 AA6 3 MET B 137 TRP B 144 1 O MET B 137 N ILE A 138 SHEET 1 AA7 3 TYR C 149 ARG C 150 0 SHEET 2 AA7 3 TYR A 149 ARG A 150 1 N ARG A 150 O TYR C 149 SHEET 3 AA7 3 TYR B 149 ARG B 150 1 O ARG B 150 N TYR A 149 SHEET 1 AA8 3 TYR C 154 ARG C 155 0 SHEET 2 AA8 3 TYR A 154 ARG A 155 1 N TYR A 154 O ARG C 155 SHEET 3 AA8 3 TYR B 154 ARG B 155 1 O TYR B 154 N ARG A 155 SHEET 1 AA9 3 ASN C 158 TYR C 162 0 SHEET 2 AA9 3 ASN A 158 TYR A 162 1 N VAL A 160 O TYR C 161 SHEET 3 AA9 3 ASN B 158 TYR B 162 1 O VAL B 160 N TYR A 161 SHEET 1 AB1 3 ASP C 166 VAL C 179 0 SHEET 2 AB1 3 ASP A 166 GLU A 195 1 N GLN A 167 O TYR C 168 SHEET 3 AB1 3 GLY C 194 GLU C 195 1 O GLY C 194 N LYS A 193 SHEET 1 AB2 3 THR C 182 THR C 191 0 SHEET 2 AB2 3 ASP A 166 GLU A 195 1 N VAL A 188 O THR C 189 SHEET 3 AB2 3 ASP B 166 GLU B 195 1 O GLN B 167 N TYR A 168 SHEET 1 AB3 3 THR C 198 GLU C 206 0 SHEET 2 AB3 3 THR A 198 GLU A 206 1 N THR A 198 O GLU C 199 SHEET 3 AB3 3 THR B 198 GLU B 206 1 O THR B 198 N GLU A 199 SHEET 1 AB4 3 GLN C 211 ASP C 226 0 SHEET 2 AB4 3 GLN A 211 ASP A 226 1 N THR A 215 O GLN C 216 SHEET 3 AB4 3 GLN B 211 ASP B 226 1 O THR B 215 N GLN A 216 SSBOND 1 CYS A 178 CYS A 213 1555 1555 2.03 SSBOND 2 CYS C 178 CYS C 213 1555 1555 2.03 SSBOND 3 CYS B 178 CYS B 213 1555 1555 2.04 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