HEADER PROTEIN FIBRIL 14-DEC-21 7QIG TITLE INFECTIOUS MOUSE-ADAPTED RML 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, B, C; 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; SOURCE 5 ORGAN: BRAIN KEYWDS PRION, AMYLOID, PRP, PRION PROTEIN, MOUSE RML SCRAPIE STRAIN, EX VIVO KEYWDS 2 PRION, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR S.W.MANKA,W.ZHANG,A.WENBORN,J.BETTS,S.JOINER,H.R.SAIBIL,J.COLLINGE, AUTHOR 2 J.D.F.WADSWORTH REVDAT 1 27-JUL-22 7QIG 0 JRNL AUTH S.W.MANKA,W.ZHANG,A.WENBORN,J.BETTS,S.JOINER,H.R.SAIBIL, JRNL AUTH 2 J.COLLINGE,J.D.F.WADSWORTH JRNL TITL 2.7 ANGSTROM CRYO-EM STRUCTURE OF EX VIVO RML PRION FIBRILS. JRNL REF NAT COMMUN V. 13 4004 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35831275 JRNL DOI 10.1038/S41467-022-30457-7 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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 : 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) : 2.700 REMARK 3 NUMBER OF PARTICLES : 119390 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 7QIG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119739. 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 MOUSE PRP REMARK 245 FROM RML--INFECTED MOUSE BRAIN 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) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 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, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS B 193 OE2 GLU B 195 2.14 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 110 60.69 62.07 REMARK 500 PHE A 140 34.22 -143.68 REMARK 500 MET A 153 66.09 61.94 REMARK 500 VAL A 165 -64.68 -92.99 REMARK 500 GLU A 206 -65.06 -91.37 REMARK 500 ARG A 207 47.19 -140.58 REMARK 500 MET A 212 -60.03 -101.55 REMARK 500 LYS B 100 59.63 -153.15 REMARK 500 HIS B 110 60.49 63.01 REMARK 500 PHE B 140 24.53 -144.13 REMARK 500 MET B 153 62.86 65.98 REMARK 500 VAL B 165 -64.79 -92.81 REMARK 500 GLU B 195 -60.12 -92.38 REMARK 500 GLU B 206 -66.63 -99.09 REMARK 500 MET B 212 -60.41 -101.90 REMARK 500 HIS C 110 61.53 61.69 REMARK 500 PHE C 140 27.43 -144.11 REMARK 500 MET C 153 64.13 64.29 REMARK 500 VAL C 165 -61.90 -92.29 REMARK 500 GLU C 195 -62.15 -95.29 REMARK 500 GLU C 206 -64.46 -91.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13989 RELATED DB: EMDB REMARK 900 INFECTIOUS MOUSE-ADAPTED RML SCRAPIE PRION FIBRIL PURIFIED FROM REMARK 900 TERMINALLY-INFECTED MOUSE BRAINS DBREF 7QIG A 94 225 UNP P04925 PRIO_MOUSE 94 225 DBREF 7QIG B 94 225 UNP P04925 PRIO_MOUSE 94 225 DBREF 7QIG C 94 225 UNP P04925 PRIO_MOUSE 94 225 SEQRES 1 A 132 THR HIS ASN GLN TRP ASN LYS PRO SER LYS PRO LYS THR SEQRES 2 A 132 ASN LEU LYS HIS VAL ALA GLY ALA ALA ALA ALA GLY ALA SEQRES 3 A 132 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA SEQRES 4 A 132 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU SEQRES 5 A 132 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN SEQRES 6 A 132 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN SEQRES 7 A 132 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS SEQRES 8 A 132 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE SEQRES 9 A 132 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU SEQRES 10 A 132 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA SEQRES 11 A 132 TYR TYR SEQRES 1 B 132 THR HIS ASN GLN TRP ASN LYS PRO SER LYS PRO LYS THR SEQRES 2 B 132 ASN LEU LYS HIS VAL ALA GLY ALA ALA ALA ALA GLY ALA SEQRES 3 B 132 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA SEQRES 4 B 132 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU SEQRES 5 B 132 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN SEQRES 6 B 132 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN SEQRES 7 B 132 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS SEQRES 8 B 132 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE SEQRES 9 B 132 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU SEQRES 10 B 132 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA SEQRES 11 B 132 TYR TYR SEQRES 1 C 132 THR HIS ASN GLN TRP ASN LYS PRO SER LYS PRO LYS THR SEQRES 2 C 132 ASN LEU LYS HIS VAL ALA GLY ALA ALA ALA ALA GLY ALA SEQRES 3 C 132 VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER ALA SEQRES 4 C 132 MET SER ARG PRO MET ILE HIS PHE GLY ASN ASP TRP GLU SEQRES 5 C 132 ASP ARG TYR TYR ARG GLU ASN MET TYR ARG TYR PRO ASN SEQRES 6 C 132 GLN VAL TYR TYR ARG PRO VAL ASP GLN TYR SER ASN GLN SEQRES 7 C 132 ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE LYS SEQRES 8 C 132 GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN PHE SEQRES 9 C 132 THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL GLU SEQRES 10 C 132 GLN MET CYS VAL THR GLN TYR GLN LYS GLU SER GLN ALA SEQRES 11 C 132 TYR TYR SHEET 1 AA1 3 HIS B 95 ASN B 99 0 SHEET 2 AA1 3 HIS A 95 ASN A 99 1 N GLN A 97 O TRP B 98 SHEET 3 AA1 3 HIS C 95 ASN C 99 1 O HIS C 95 N ASN A 96 SHEET 1 AA2 3 LYS B 105 ALA B 115 0 SHEET 2 AA2 3 LYS A 105 ALA A 115 1 N LEU A 108 O ASN B 107 SHEET 3 AA2 3 LYS C 105 ALA C 115 1 O ALA C 114 N ALA A 115 SHEET 1 AA3 3 VAL B 120 VAL B 121 0 SHEET 2 AA3 3 VAL A 120 VAL A 121 1 N VAL A 121 O VAL B 120 SHEET 3 AA3 3 VAL C 120 VAL C 121 1 O VAL C 121 N VAL A 120 SHEET 1 AA4 3 TYR B 127 SER B 134 0 SHEET 2 AA4 3 TYR A 127 SER A 134 1 N TYR A 127 O MET B 128 SHEET 3 AA4 3 TYR C 127 SER C 134 1 O TYR C 127 N MET A 128 SHEET 1 AA5 3 MET B 137 HIS B 139 0 SHEET 2 AA5 3 MET A 137 HIS A 139 1 N ILE A 138 O HIS B 139 SHEET 3 AA5 3 MET C 137 HIS C 139 1 O ILE C 138 N HIS A 139 SHEET 1 AA6 3 ASN B 142 ASP B 146 0 SHEET 2 AA6 3 ASN A 142 ASP A 146 1 N TRP A 144 O GLU B 145 SHEET 3 AA6 3 ASN C 142 ASP C 146 1 O TRP C 144 N GLU A 145 SHEET 1 AA7 3 TYR B 149 ARG B 150 0 SHEET 2 AA7 3 TYR A 149 ARG A 150 1 N TYR A 149 O ARG B 150 SHEET 3 AA7 3 TYR C 149 ARG C 150 1 O TYR C 149 N ARG A 150 SHEET 1 AA8 3 TYR B 154 ARG B 155 0 SHEET 2 AA8 3 TYR A 154 ARG A 155 1 N ARG A 155 O TYR B 154 SHEET 3 AA8 3 TYR C 154 ARG C 155 1 O ARG C 155 N TYR A 154 SHEET 1 AA9 3 ASN B 158 TYR B 162 0 SHEET 2 AA9 3 ASN A 158 TYR A 162 1 N TYR A 161 O TYR B 162 SHEET 3 AA9 3 ASN C 158 TYR C 162 1 O TYR C 161 N TYR A 162 SHEET 1 AB1 3 ASP B 166 ASN B 172 0 SHEET 2 AB1 3 ASP A 166 ASN A 172 1 N TYR A 168 O GLN B 167 SHEET 3 AB1 3 ASP C 166 ASN C 172 1 O TYR C 168 N GLN A 167 SHEET 1 AB2 3 VAL B 175 THR B 191 0 SHEET 2 AB2 3 VAL A 175 MET A 205 1 N ILE A 181 O THR B 182 SHEET 3 AB2 3 GLY B 194 MET B 205 1 O ASN B 196 N GLU A 195 SHEET 1 AB3 3 VAL B 175 THR B 191 0 SHEET 2 AB3 3 VAL A 175 MET A 205 1 N ILE A 181 O THR B 182 SHEET 3 AB3 3 VAL C 175 MET C 205 1 O GLU C 195 N ASN A 196 SHEET 1 AB4 3 GLN B 211 LYS B 219 0 SHEET 2 AB4 3 GLN A 211 LYS A 219 1 N GLN A 216 O THR B 215 SHEET 3 AB4 3 GLN C 211 LYS C 219 1 O GLN C 216 N THR A 215 SHEET 1 AB5 3 GLN B 222 TYR B 224 0 SHEET 2 AB5 3 GLN A 222 TYR A 224 1 N ALA A 223 O TYR B 224 SHEET 3 AB5 3 GLN C 222 TYR C 224 1 O ALA C 223 N TYR A 224 SSBOND 1 CYS A 178 CYS A 213 1555 1555 2.03 SSBOND 2 CYS B 178 CYS B 213 1555 1555 2.03 SSBOND 3 CYS C 178 CYS C 213 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