HEADER PROTEIN FIBRIL 11-MAR-22 7X84 TITLE CRYO-EM STRUCTURE OF THE TMEM106B FIBRIL FROM PARKINSON'S DISEASE TITLE 2 DEMENTIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE PROTEIN 106B; COMPND 3 CHAIN: B, A, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS PROTEIN FIBRIL, AMYLOID EXPDTA ELECTRON MICROSCOPY AUTHOR Q.Y.ZHAO,W.C.XIA,Y.FAN,Y.P.SUN,Y.Q.TAO,C.LIU REVDAT 1 15-JUN-22 7X84 0 JRNL AUTH Y.FAN,Q.ZHAO,W.XIA,Y.TAO,W.YU,M.CHEN,Y.LIU,J.ZHAO,Y.SHEN, JRNL AUTH 2 Y.SUN,C.SI,S.ZHANG,Y.ZHANG,W.LI,C.LIU,J.WANG,D.LI JRNL TITL GENERIC AMYLOID FIBRILLATION OF TMEM106B IN PATIENT WITH JRNL TITL 2 PARKINSON'S DISEASE DEMENTIA AND NORMAL ELDERS. JRNL REF CELL RES. V. 32 585 2022 JRNL REFN ISSN 1001-0602 JRNL PMID 35477998 JRNL DOI 10.1038/S41422-022-00665-3 REMARK 2 REMARK 2 RESOLUTION. 3.00 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 : 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) : 3.000 REMARK 3 NUMBER OF PARTICLES : 17752 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7X84 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028293. 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 : THE FIBRIL FORMED BY TMEM106B REMARK 245 FROM PARKINSON'S DISEASE REMARK 245 DEMENTIA 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 : 7.40 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) : 1400.00 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 : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5500.00 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: B, A, 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: 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 B 122 61.85 62.26 REMARK 500 VAL B 128 -64.98 -125.91 REMARK 500 GLN B 138 -64.46 -100.30 REMARK 500 ARG B 140 17.55 55.76 REMARK 500 LEU B 144 114.80 -161.07 REMARK 500 THR B 174 136.35 -170.60 REMARK 500 LEU B 190 62.19 64.78 REMARK 500 GLU B 206 115.91 -160.03 REMARK 500 ASN B 223 -53.66 -120.30 REMARK 500 THR B 231 -168.86 -126.31 REMARK 500 GLN B 249 117.03 -160.57 REMARK 500 ASP A 122 61.76 62.28 REMARK 500 VAL A 128 -64.96 -125.90 REMARK 500 GLN A 138 -64.39 -100.38 REMARK 500 ARG A 140 17.57 55.77 REMARK 500 LEU A 144 114.82 -161.06 REMARK 500 THR A 174 136.27 -170.72 REMARK 500 LEU A 190 62.24 64.76 REMARK 500 ASN A 223 -53.75 -120.24 REMARK 500 THR A 231 -168.86 -126.37 REMARK 500 GLN A 249 117.06 -160.58 REMARK 500 ASP C 122 61.84 62.29 REMARK 500 VAL C 128 -64.97 -125.81 REMARK 500 GLN C 138 -64.42 -100.29 REMARK 500 ARG C 140 17.56 55.67 REMARK 500 LEU C 144 114.78 -161.06 REMARK 500 THR C 174 136.33 -170.65 REMARK 500 LEU C 190 62.22 64.76 REMARK 500 GLU C 206 115.90 -160.04 REMARK 500 ASN C 223 -53.77 -120.27 REMARK 500 THR C 231 -168.87 -126.31 REMARK 500 GLN C 249 117.02 -160.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33055 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE TMEM106B FIBRIL FROM PARKINSON'S DISEASE REMARK 900 DEMENTIA DBREF 7X84 B 120 254 UNP Q9NUM4 T106B_HUMAN 120 254 DBREF 7X84 A 120 254 UNP Q9NUM4 T106B_HUMAN 120 254 DBREF 7X84 C 120 254 UNP Q9NUM4 T106B_HUMAN 120 254 SEQRES 1 B 135 SER ILE ASP VAL LYS TYR ILE GLY VAL LYS SER ALA TYR SEQRES 2 B 135 VAL SER TYR ASP VAL GLN LYS ARG THR ILE TYR LEU ASN SEQRES 3 B 135 ILE THR ASN THR LEU ASN ILE THR ASN ASN ASN TYR TYR SEQRES 4 B 135 SER VAL GLU VAL GLU ASN ILE THR ALA GLN VAL GLN PHE SEQRES 5 B 135 SER LYS THR VAL ILE GLY LYS ALA ARG LEU ASN ASN ILE SEQRES 6 B 135 THR ILE ILE GLY PRO LEU ASP MET LYS GLN ILE ASP TYR SEQRES 7 B 135 THR VAL PRO THR VAL ILE ALA GLU GLU MET SER TYR MET SEQRES 8 B 135 TYR ASP PHE CYS THR LEU ILE SER ILE LYS VAL HIS ASN SEQRES 9 B 135 ILE VAL LEU MET MET GLN VAL THR VAL THR THR THR TYR SEQRES 10 B 135 PHE GLY HIS SER GLU GLN ILE SER GLN GLU ARG TYR GLN SEQRES 11 B 135 TYR VAL ASP CYS GLY SEQRES 1 A 135 SER ILE ASP VAL LYS TYR ILE GLY VAL LYS SER ALA TYR SEQRES 2 A 135 VAL SER TYR ASP VAL GLN LYS ARG THR ILE TYR LEU ASN SEQRES 3 A 135 ILE THR ASN THR LEU ASN ILE THR ASN ASN ASN TYR TYR SEQRES 4 A 135 SER VAL GLU VAL GLU ASN ILE THR ALA GLN VAL GLN PHE SEQRES 5 A 135 SER LYS THR VAL ILE GLY LYS ALA ARG LEU ASN ASN ILE SEQRES 6 A 135 THR ILE ILE GLY PRO LEU ASP MET LYS GLN ILE ASP TYR SEQRES 7 A 135 THR VAL PRO THR VAL ILE ALA GLU GLU MET SER TYR MET SEQRES 8 A 135 TYR ASP PHE CYS THR LEU ILE SER ILE LYS VAL HIS ASN SEQRES 9 A 135 ILE VAL LEU MET MET GLN VAL THR VAL THR THR THR TYR SEQRES 10 A 135 PHE GLY HIS SER GLU GLN ILE SER GLN GLU ARG TYR GLN SEQRES 11 A 135 TYR VAL ASP CYS GLY SEQRES 1 C 135 SER ILE ASP VAL LYS TYR ILE GLY VAL LYS SER ALA TYR SEQRES 2 C 135 VAL SER TYR ASP VAL GLN LYS ARG THR ILE TYR LEU ASN SEQRES 3 C 135 ILE THR ASN THR LEU ASN ILE THR ASN ASN ASN TYR TYR SEQRES 4 C 135 SER VAL GLU VAL GLU ASN ILE THR ALA GLN VAL GLN PHE SEQRES 5 C 135 SER LYS THR VAL ILE GLY LYS ALA ARG LEU ASN ASN ILE SEQRES 6 C 135 THR ILE ILE GLY PRO LEU ASP MET LYS GLN ILE ASP TYR SEQRES 7 C 135 THR VAL PRO THR VAL ILE ALA GLU GLU MET SER TYR MET SEQRES 8 C 135 TYR ASP PHE CYS THR LEU ILE SER ILE LYS VAL HIS ASN SEQRES 9 C 135 ILE VAL LEU MET MET GLN VAL THR VAL THR THR THR TYR SEQRES 10 C 135 PHE GLY HIS SER GLU GLN ILE SER GLN GLU ARG TYR GLN SEQRES 11 C 135 TYR VAL ASP CYS GLY SHEET 1 AA1 3 TYR B 125 ILE B 126 0 SHEET 2 AA1 3 TYR A 125 ILE A 126 1 O TYR A 125 N ILE B 126 SHEET 3 AA1 3 TYR C 125 ILE C 126 1 O TYR C 125 N ILE A 126 SHEET 1 AA2 3 LYS B 129 SER B 130 0 SHEET 2 AA2 3 LYS A 129 SER A 130 1 O LYS A 129 N SER B 130 SHEET 3 AA2 3 LYS C 129 SER C 130 1 O LYS C 129 N SER A 130 SHEET 1 AA3 3 VAL B 133 SER B 134 0 SHEET 2 AA3 3 VAL A 133 SER A 134 1 O SER A 134 N VAL B 133 SHEET 3 AA3 3 VAL C 133 SER C 134 1 O SER C 134 N VAL A 133 SHEET 1 AA4 3 VAL B 137 LYS B 139 0 SHEET 2 AA4 3 VAL A 137 LYS A 139 1 O LYS A 139 N GLN B 138 SHEET 3 AA4 3 VAL C 137 LYS C 139 1 O LYS C 139 N GLN A 138 SHEET 1 AA5 3 ASN B 151 ILE B 152 0 SHEET 2 AA5 3 ASN A 151 ILE A 152 1 O ASN A 151 N ILE B 152 SHEET 3 AA5 3 ASN C 151 ILE C 152 1 O ASN C 151 N ILE A 152 SHEET 1 AA6 3 VAL B 162 GLN B 168 0 SHEET 2 AA6 3 VAL A 162 GLN A 168 1 O ASN A 164 N ILE B 165 SHEET 3 AA6 3 VAL C 162 GLN C 168 1 O ASN C 164 N ILE A 165 SHEET 1 AA7 3 VAL B 175 GLY B 177 0 SHEET 2 AA7 3 VAL A 175 GLY A 177 1 O GLY A 177 N ILE B 176 SHEET 3 AA7 3 VAL C 175 GLY C 177 1 O GLY C 177 N ILE A 176 SHEET 1 AA8 3 ARG B 180 ILE B 186 0 SHEET 2 AA8 3 ARG A 180 ILE A 186 1 O ASN A 182 N LEU B 181 SHEET 3 AA8 3 ARG C 180 ILE C 186 1 O ASN C 182 N LEU A 181 SHEET 1 AA9 3 TYR B 197 THR B 198 0 SHEET 2 AA9 3 TYR A 197 THR A 198 1 O THR A 198 N TYR B 197 SHEET 3 AA9 3 TYR C 197 THR C 198 1 O THR C 198 N TYR A 197 SHEET 1 AB1 3 THR B 201 ILE B 203 0 SHEET 2 AB1 3 THR A 201 ILE A 203 1 O VAL A 202 N ILE B 203 SHEET 3 AB1 3 THR C 201 ILE C 203 1 O VAL C 202 N ILE A 203 SHEET 1 AB2 3 THR B 215 VAL B 221 0 SHEET 2 AB2 3 THR A 215 VAL A 221 1 O LYS A 220 N ILE B 219 SHEET 3 AB2 3 THR C 215 VAL C 221 1 O LYS C 220 N ILE A 219 SHEET 1 AB3 3 LEU B 226 MET B 228 0 SHEET 2 AB3 3 LEU A 226 MET A 228 1 O LEU A 226 N MET B 227 SHEET 3 AB3 3 LEU C 226 MET C 228 1 O LEU C 226 N MET A 227 SHEET 1 AB4 3 THR B 235 GLY B 238 0 SHEET 2 AB4 3 THR A 235 GLY A 238 1 O GLY A 238 N PHE B 237 SHEET 3 AB4 3 THR C 235 GLY C 238 1 O GLY C 238 N PHE A 237 SHEET 1 AB5 3 ILE B 243 ARG B 247 0 SHEET 2 AB5 3 ILE A 243 ARG A 247 1 O SER A 244 N GLN B 245 SHEET 3 AB5 3 ILE C 243 ARG C 247 1 O SER C 244 N GLN A 245 SHEET 1 AB6 3 VAL B 251 ASP B 252 0 SHEET 2 AB6 3 VAL A 251 ASP A 252 1 O VAL A 251 N ASP B 252 SHEET 3 AB6 3 VAL C 251 ASP C 252 1 O VAL C 251 N ASP A 252 SSBOND 1 CYS B 214 CYS B 253 1555 1555 2.02 SSBOND 2 CYS A 214 CYS A 253 1555 1555 2.02 SSBOND 3 CYS C 214 CYS C 253 1555 1555 2.02 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