HEADER PROTEIN FIBRIL 06-FEB-21 7LNA TITLE INFECTIOUS MAMMALIAN PRION FIBRIL (263K SCRAPIE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PRP,PRP27-30,PRP33-35C; COMPND 5 OTHER_DETAILS: PROTEASE-RESISTANT GLYCOSYLATED, COMPND 6 GLYCOPHOPHATIDLYINOSITOL-ANCHORED INFECTIOUS PRION AMYLOID CORE COMPND 7 (INCLUSIVE OF RESIDUES 90-231). SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESOCRICETUS AURATUS; SOURCE 3 ORGANISM_COMMON: GOLDEN HAMSTER; SOURCE 4 ORGANISM_TAXID: 10036; SOURCE 5 ORGAN: BRAIN KEYWDS INFECTIOUS MAMMALIAN PRION, TEMPLATING, GLYCOSYLATED KEYWDS 2 GLYCOPHOPHATIDLYINOSITOL-ANCHORED AMYLOID, PIRIBS, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR A.KRAUS,F.HOYT,C.L.SCHWARTZ,B.HANSEN,A.G.HUGHSON,E.ARTIKIS,B.RACE, AUTHOR 2 B.CAUGHEY REVDAT 3 17-NOV-21 7LNA 1 JRNL REVDAT 2 08-SEP-21 7LNA 1 JRNL REVDAT 1 01-SEP-21 7LNA 0 JRNL AUTH A.KRAUS,F.HOYT,C.L.SCHWARTZ,B.HANSEN,E.ARTIKIS,A.G.HUGHSON, JRNL AUTH 2 G.J.RAYMOND,B.RACE,G.S.BARON,B.CAUGHEY JRNL TITL HIGH-RESOLUTION STRUCTURE AND STRAIN COMPARISON OF JRNL TITL 2 INFECTIOUS MAMMALIAN PRIONS. JRNL REF MOL.CELL V. 81 4540 2021 JRNL REFN ISSN 1097-2765 JRNL PMID 34433091 JRNL DOI 10.1016/J.MOLCEL.2021.08.011 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, SERIALEM, CTFFIND, COOT, REMARK 3 PHENIX, PHENIX, REFMAC, RELION, RELION, REMARK 3 RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : RECIPROCAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.140 REMARK 3 NUMBER OF PARTICLES : 15884 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: AUTO-REFINEMENT WAS THEN PERFORMED WHILE OPTIMIZING REMARK 3 THE HELICAL TWIST AND RISE. AUTO-REFINEMENT WITH REFINEMENT OF REMARK 3 TWIST AND RISE YIELDED A FINAL MAP WITH A TWIST OF -0.847 DEGREE REMARK 3 AND RISE OF 4.874 ANGSTROM. ITERATIVE CYCLES OF CTF REFINEMENT, REMARK 3 BAYESIAN POLISHING, AND AUTO REFINEMENT WERE USED UNTIL REMARK 3 RESOLUTION ESTIMATES STABILIZED. POST PROCESSING IN RELION WAS REMARK 3 PERFORMED WITH A SOFT-EDGED MASK REPRESENTING 10% OF THE CENTRAL REMARK 3 Z LENGTH OF THE FIBRIL. SHARPENING WAS APPLIED WITH A B-FACTOR REMARK 3 OF -31 SQUARE ANGSTROM. REMARK 4 REMARK 4 7LNA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254649. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : FILAMENT REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : INFECTIOUS MAMMALIAN PRION REMARK 245 FIBRIL (263K SCRAPIE) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : SOLARUS 950 (GATAN, PLEASANTON REMARK 245 CA) REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : PURIFIED FROM BRAINS OF REMARK 245 HAMSTERS WITH CLINICAL SCRAPIE PRION DISEASE. 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 BIOQUANTUM (6K X REMARK 245 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) : 6000.00 REMARK 245 ILLUMINATION MODE : OTHER 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, B, C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 90 REMARK 465 GLN A 91 REMARK 465 GLY A 92 REMARK 465 GLY A 93 REMARK 465 GLY A 94 REMARK 465 LYS A 194 REMARK 465 GLY A 195 REMARK 465 GLU A 196 REMARK 465 GLY A 228 REMARK 465 ARG A 229 REMARK 465 ARG A 230 REMARK 465 SER A 231 REMARK 465 GLY B 90 REMARK 465 GLN B 91 REMARK 465 GLY B 92 REMARK 465 GLY B 93 REMARK 465 GLY B 94 REMARK 465 LYS B 194 REMARK 465 GLY B 195 REMARK 465 GLU B 196 REMARK 465 GLY B 228 REMARK 465 ARG B 229 REMARK 465 ARG B 230 REMARK 465 SER B 231 REMARK 465 GLY C 90 REMARK 465 GLN C 91 REMARK 465 GLY C 92 REMARK 465 GLY C 93 REMARK 465 GLY C 94 REMARK 465 LYS C 194 REMARK 465 GLY C 195 REMARK 465 GLU C 196 REMARK 465 GLY C 228 REMARK 465 ARG C 229 REMARK 465 ARG C 230 REMARK 465 SER C 231 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 ASP A 147 -64.09 -98.37 REMARK 500 ASP B 147 -64.40 -98.63 REMARK 500 ASP C 147 -63.66 -98.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-23459 RELATED DB: EMDB REMARK 900 INFECTIOUS MAMMALIAN PRION FIBRIL (263K SCRAPIE) DBREF 7LNA A 90 231 UNP P04273 PRIO_MESAU 90 231 DBREF 7LNA B 90 231 UNP P04273 PRIO_MESAU 90 231 DBREF 7LNA C 90 231 UNP P04273 PRIO_MESAU 90 231 SEQRES 1 A 142 GLY GLN GLY GLY GLY THR HIS ASN GLN TRP ASN LYS PRO SEQRES 2 A 142 SER LYS PRO LYS THR ASN MET LYS HIS MET ALA GLY ALA SEQRES 3 A 142 ALA ALA ALA GLY ALA VAL VAL GLY GLY LEU GLY GLY TYR SEQRES 4 A 142 MET LEU GLY SER ALA MET SER ARG PRO MET MET HIS PHE SEQRES 5 A 142 GLY ASN ASP TRP GLU ASP ARG TYR TYR ARG GLU ASN MET SEQRES 6 A 142 ASN ARG TYR PRO ASN GLN VAL TYR TYR ARG PRO VAL ASP SEQRES 7 A 142 GLN TYR ASN ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL SEQRES 8 A 142 ASN ILE THR ILE LYS GLN HIS THR VAL THR THR THR THR SEQRES 9 A 142 LYS GLY GLU ASN PHE THR GLU THR ASP ILE LYS ILE MET SEQRES 10 A 142 GLU ARG VAL VAL GLU GLN MET CYS THR THR GLN TYR GLN SEQRES 11 A 142 LYS GLU SER GLN ALA TYR TYR ASP GLY ARG ARG SER SEQRES 1 B 142 GLY GLN GLY GLY GLY THR HIS ASN GLN TRP ASN LYS PRO SEQRES 2 B 142 SER LYS PRO LYS THR ASN MET LYS HIS MET ALA GLY ALA SEQRES 3 B 142 ALA ALA ALA GLY ALA VAL VAL GLY GLY LEU GLY GLY TYR SEQRES 4 B 142 MET LEU GLY SER ALA MET SER ARG PRO MET MET HIS PHE SEQRES 5 B 142 GLY ASN ASP TRP GLU ASP ARG TYR TYR ARG GLU ASN MET SEQRES 6 B 142 ASN ARG TYR PRO ASN GLN VAL TYR TYR ARG PRO VAL ASP SEQRES 7 B 142 GLN TYR ASN ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL SEQRES 8 B 142 ASN ILE THR ILE LYS GLN HIS THR VAL THR THR THR THR SEQRES 9 B 142 LYS GLY GLU ASN PHE THR GLU THR ASP ILE LYS ILE MET SEQRES 10 B 142 GLU ARG VAL VAL GLU GLN MET CYS THR THR GLN TYR GLN SEQRES 11 B 142 LYS GLU SER GLN ALA TYR TYR ASP GLY ARG ARG SER SEQRES 1 C 142 GLY GLN GLY GLY GLY THR HIS ASN GLN TRP ASN LYS PRO SEQRES 2 C 142 SER LYS PRO LYS THR ASN MET LYS HIS MET ALA GLY ALA SEQRES 3 C 142 ALA ALA ALA GLY ALA VAL VAL GLY GLY LEU GLY GLY TYR SEQRES 4 C 142 MET LEU GLY SER ALA MET SER ARG PRO MET MET HIS PHE SEQRES 5 C 142 GLY ASN ASP TRP GLU ASP ARG TYR TYR ARG GLU ASN MET SEQRES 6 C 142 ASN ARG TYR PRO ASN GLN VAL TYR TYR ARG PRO VAL ASP SEQRES 7 C 142 GLN TYR ASN ASN GLN ASN ASN PHE VAL HIS ASP CYS VAL SEQRES 8 C 142 ASN ILE THR ILE LYS GLN HIS THR VAL THR THR THR THR SEQRES 9 C 142 LYS GLY GLU ASN PHE THR GLU THR ASP ILE LYS ILE MET SEQRES 10 C 142 GLU ARG VAL VAL GLU GLN MET CYS THR THR GLN TYR GLN SEQRES 11 C 142 LYS GLU SER GLN ALA TYR TYR ASP GLY ARG ARG SER SHEET 1 AA1 3 HIS B 96 GLN B 98 0 SHEET 2 AA1 3 HIS A 96 GLN A 98 1 N ASN A 97 O HIS B 96 SHEET 3 AA1 3 HIS C 96 GLN C 98 1 O ASN C 97 N HIS A 96 SHEET 1 AA2 3 LYS B 106 ASN B 108 0 SHEET 2 AA2 3 LYS A 106 ASN A 108 1 N LYS A 106 O THR B 107 SHEET 3 AA2 3 LYS C 106 ASN C 108 1 O LYS C 106 N THR A 107 SHEET 1 AA3 3 ALA B 115 ALA B 118 0 SHEET 2 AA3 3 ALA A 115 ALA A 118 1 N ALA A 116 O ALA B 115 SHEET 3 AA3 3 ALA C 115 ALA C 118 1 O ALA C 116 N ALA A 115 SHEET 1 AA4 3 MET B 138 HIS B 140 0 SHEET 2 AA4 3 MET A 138 HIS A 140 1 N MET A 138 O MET B 139 SHEET 3 AA4 3 MET C 138 HIS C 140 1 O MET C 138 N MET A 139 SHEET 1 AA5 3 TYR B 150 ARG B 151 0 SHEET 2 AA5 3 TYR A 150 ARG A 151 1 N ARG A 151 O TYR B 150 SHEET 3 AA5 3 TYR C 150 ARG C 151 1 O ARG C 151 N TYR A 150 SHEET 1 AA6 3 ASN B 159 TYR B 163 0 SHEET 2 AA6 3 ASN A 159 TYR A 163 1 N ASN A 159 O GLN B 160 SHEET 3 AA6 3 ASN C 159 TYR C 163 1 O ASN C 159 N GLN A 160 SHEET 1 AA7 3 VAL B 166 GLN B 168 0 SHEET 2 AA7 3 VAL A 166 GLN A 168 1 N ASP A 167 O VAL B 166 SHEET 3 AA7 3 VAL C 166 GLN C 168 1 O ASP C 167 N VAL A 166 SHEET 1 AA8 3 ASN B 171 VAL B 176 0 SHEET 2 AA8 3 ASN A 171 VAL A 176 1 N ASN A 174 O PHE B 175 SHEET 3 AA8 3 ASN C 171 VAL C 176 1 O ASN C 174 N PHE A 175 SHEET 1 AA9 3 VAL B 180 LYS B 185 0 SHEET 2 AA9 3 VAL A 180 LYS A 185 1 N THR A 183 O ILE B 182 SHEET 3 AA9 3 VAL C 180 LYS C 185 1 O THR C 183 N ILE A 182 SHEET 1 AB1 3 THR B 188 THR B 191 0 SHEET 2 AB1 3 THR A 188 THR A 191 1 N VAL A 189 O THR B 188 SHEET 3 AB1 3 THR C 188 THR C 191 1 O VAL C 189 N THR A 188 SHEET 1 AB2 3 PHE B 198 THR B 199 0 SHEET 2 AB2 3 PHE A 198 THR A 199 1 N THR A 199 O PHE B 198 SHEET 3 AB2 3 PHE C 198 THR C 199 1 O THR C 199 N PHE A 198 SHEET 1 AB3 3 ASP B 202 ILE B 205 0 SHEET 2 AB3 3 ASP A 202 ILE A 205 1 N ILE A 203 O ASP B 202 SHEET 3 AB3 3 ASP C 202 ILE C 205 1 O ILE C 203 N ASP A 202 SHEET 1 AB4 3 GLN B 223 TYR B 225 0 SHEET 2 AB4 3 GLN A 223 TYR A 225 1 N ALA A 224 O GLN B 223 SHEET 3 AB4 3 GLN C 223 TYR C 225 1 O ALA C 224 N GLN A 223 SSBOND 1 CYS A 179 CYS A 214 1555 1555 2.03 SSBOND 2 CYS B 179 CYS B 214 1555 1555 2.03 SSBOND 3 CYS C 179 CYS C 214 1555 1555 2.03 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