HEADER TRANSPORT PROTEIN 19-FEB-22 7U15 TITLE TMEM106B(120-254) SINGLET AMYLOID FIBRIL FROM FRONTOTEMPORAL LOBAR TITLE 2 DEGENERATION WITH TDP-43 PATHOLOGY (FTLD-TDP) TYPE B CASE 2 (CASE 7). COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE PROTEIN 106B; COMPND 3 CHAIN: B, A, C; COMPND 4 FRAGMENT: UNP RESIDUES 120-254; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TMEM106B; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS TMEM106B, AMYLOID FIBRIL, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.W.P.FITZPATRICK,M.H.B.STOWELL,A.CHANG,X.XIANG,J.WANG,C.LEE, AUTHOR 2 T.ARAKHAMIA,M.SIMJANOSKA,C.WANG,Y.CARLOMAGNO,G.ZHANG,S.DHINGRA, AUTHOR 3 M.THIERRY,J.PERNEEL,B.HEEMAN,L.M.FORGRAVE,M.DETURE,M.L.DEMARCO, AUTHOR 4 C.N.COOK,R.RADEMAKERS,D.DICKSON,L.PETRUCELLI,I.R.A.MACKENZIE REVDAT 2 27-APR-22 7U15 1 JRNL REVDAT 1 23-MAR-22 7U15 0 JRNL AUTH A.CHANG,X.XIANG,J.WANG,C.LEE,T.ARAKHAMIA,M.SIMJANOSKA, JRNL AUTH 2 C.WANG,Y.CARLOMAGNO,G.ZHANG,S.DHINGRA,M.THIERRY,J.PERNEEL, JRNL AUTH 3 B.HEEMAN,L.M.FORGRAVE,M.DETURE,M.L.DEMARCO,C.N.COOK, JRNL AUTH 4 R.RADEMAKERS,D.W.DICKSON,L.PETRUCELLI,M.H.B.STOWELL, JRNL AUTH 5 I.R.A.MACKENZIE,A.W.P.FITZPATRICK JRNL TITL HOMOTYPIC FIBRILLIZATION OF TMEM106B ACROSS DIVERSE JRNL TITL 2 NEURODEGENERATIVE DISEASES. JRNL REF CELL V. 185 1346 2022 JRNL REFN ISSN 1097-4172 JRNL PMID 35247328 JRNL DOI 10.1016/J.CELL.2022.02.026 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 : 31000 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 7U15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000263349. 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 : TMEM106B(120-254) SINGLET REMARK 245 AMYLOID FIBRIL FROM DEMENTIA REMARK 245 WITH LEWY BODIES (DLB). 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 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1400.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2800.00 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) : 6000.00 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: 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 H VAL B 128 O VAL C 128 1.59 REMARK 500 OG SER A 120 OE2 GLU C 241 1.89 REMARK 500 OH TYR B 248 O GLY A 127 2.12 REMARK 500 ND2 ASN B 145 O5 NAG B 302 2.14 REMARK 500 ND2 ASN A 145 O5 NAG A 302 2.14 REMARK 500 ND2 ASN C 145 O5 NAG C 302 2.14 REMARK 500 O GLY B 127 OH TYR C 248 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26278 RELATED DB: EMDB REMARK 900 TMEM106B(120-254) SINGLET AMYLOID FIBRIL FROM FRONTOTEMPORAL LOBAR REMARK 900 DEGENERATION WITH TDP-43 PATHOLOGY (FTLD-TDP) TYPE B CASE 2 (CASE 7) REMARK 900 . DBREF 7U15 B 120 254 UNP Q9NUM4 T106B_HUMAN 120 254 DBREF 7U15 A 120 254 UNP Q9NUM4 T106B_HUMAN 120 254 DBREF 7U15 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 HET NAG B 301 14 HET NAG B 302 14 HET NAG B 303 14 HET NAG B 304 14 HET NAG A 301 14 HET NAG A 302 14 HET NAG A 303 14 HET NAG A 304 14 HET NAG C 301 14 HET NAG C 302 14 HET NAG C 303 14 HET NAG C 304 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG 12(C8 H15 N O6) SHEET 1 AA1 3 ASP A 122 VAL A 123 0 SHEET 2 AA1 3 ASP B 122 LYS B 124 1 N ASP B 122 O VAL A 123 SHEET 3 AA1 3 ASP C 122 LYS C 124 1 O ASP C 122 N VAL B 123 SHEET 1 AA2 3 LYS A 129 SER A 130 0 SHEET 2 AA2 3 LYS B 129 SER B 130 1 N SER B 130 O LYS A 129 SHEET 3 AA2 3 LYS C 129 SER C 130 1 O SER C 130 N LYS B 129 SHEET 1 AA3 3 VAL A 133 SER A 134 0 SHEET 2 AA3 3 VAL B 133 SER B 134 1 N VAL B 133 O SER A 134 SHEET 3 AA3 3 VAL C 133 SER C 134 1 O VAL C 133 N SER B 134 SHEET 1 AA4 3 TYR A 143 LEU A 144 0 SHEET 2 AA4 3 TYR B 143 LEU B 144 1 N TYR B 143 O LEU A 144 SHEET 3 AA4 3 TYR C 143 LEU C 144 1 O TYR C 143 N LEU B 144 SHEET 1 AA5 3 LEU A 150 ILE A 152 0 SHEET 2 AA5 3 LEU B 150 ILE B 152 1 N LEU B 150 O ASN A 151 SHEET 3 AA5 3 LEU C 150 ILE C 152 1 O LEU C 150 N ASN B 151 SHEET 1 AA6 3 ASN A 156 TYR A 158 0 SHEET 2 AA6 3 ASN B 156 TYR B 158 1 N ASN B 156 O TYR A 157 SHEET 3 AA6 3 ASN C 156 TYR C 158 1 O ASN C 156 N TYR B 157 SHEET 1 AA7 3 VAL A 169 PHE A 171 0 SHEET 2 AA7 3 VAL B 169 PHE B 171 1 N VAL B 169 O GLN A 170 SHEET 3 AA7 3 GLN C 170 PHE C 171 1 O PHE C 171 N GLN B 170 SHEET 1 AA8 3 THR A 185 ILE A 186 0 SHEET 2 AA8 3 THR B 185 ILE B 186 1 N THR B 185 O ILE A 186 SHEET 3 AA8 3 THR C 185 ILE C 186 1 O THR C 185 N ILE B 186 SHEET 1 AA9 3 LEU A 190 ASP A 191 0 SHEET 2 AA9 3 LEU B 190 ASP B 191 1 N LEU B 190 O ASP A 191 SHEET 3 AA9 3 LEU C 190 ASP C 191 1 O LEU C 190 N ASP B 191 SHEET 1 AB1 3 ILE A 195 ASP A 196 0 SHEET 2 AB1 3 ILE B 195 ASP B 196 1 N ILE B 195 O ASP A 196 SHEET 3 AB1 3 ILE C 195 ASP C 196 1 O ILE C 195 N ASP B 196 SHEET 1 AB2 3 GLU A 206 MET A 207 0 SHEET 2 AB2 3 GLU B 206 MET B 207 1 N GLU B 206 O MET A 207 SHEET 3 AB2 3 GLU C 206 MET C 207 1 O GLU C 206 N MET B 207 SHEET 1 AB3 3 MET A 210 ASP A 212 0 SHEET 2 AB3 3 MET B 210 ASP B 212 1 N ASP B 212 O TYR A 211 SHEET 3 AB3 3 MET C 210 ASP C 212 1 O ASP C 212 N TYR B 211 SHEET 1 AB4 3 ILE A 217 ILE A 219 0 SHEET 2 AB4 3 ILE B 217 ILE B 219 1 N ILE B 219 O SER A 218 SHEET 3 AB4 3 ILE C 217 ILE C 219 1 O ILE C 219 N SER B 218 SHEET 1 AB5 3 ILE A 224 THR A 231 0 SHEET 2 AB5 3 ILE B 224 THR B 231 1 N MET B 228 O MET A 227 SHEET 3 AB5 3 ILE C 224 THR C 231 1 O MET C 228 N MET B 227 SHEET 1 AB6 3 THR A 235 TYR A 236 0 SHEET 2 AB6 3 THR B 235 TYR B 236 1 N THR B 235 O TYR A 236 SHEET 3 AB6 3 THR C 235 TYR C 236 1 O THR C 235 N TYR B 236 SSBOND 1 CYS B 214 CYS B 253 1555 1555 2.03 SSBOND 2 CYS A 214 CYS A 253 1555 1555 2.03 SSBOND 3 CYS C 214 CYS C 253 1555 1555 2.03 LINK ND2 ASN B 145 C1 NAG B 302 1555 1555 1.44 LINK ND2 ASN B 151 C1 NAG B 303 1555 1555 1.44 LINK ND2 ASN B 164 C1 NAG B 304 1555 1555 1.44 LINK ND2 ASN B 183 C1 NAG B 301 1555 1555 1.44 LINK ND2 ASN A 145 C1 NAG A 302 1555 1555 1.44 LINK ND2 ASN A 151 C1 NAG A 303 1555 1555 1.44 LINK ND2 ASN A 164 C1 NAG A 304 1555 1555 1.44 LINK ND2 ASN A 183 C1 NAG A 301 1555 1555 1.44 LINK ND2 ASN C 145 C1 NAG C 302 1555 1555 1.44 LINK ND2 ASN C 151 C1 NAG C 303 1555 1555 1.44 LINK ND2 ASN C 164 C1 NAG C 304 1555 1555 1.44 LINK ND2 ASN C 183 C1 NAG C 301 1555 1555 1.44 CISPEP 1 GLY B 188 PRO B 189 0 0.25 CISPEP 2 GLY A 188 PRO A 189 0 0.17 CISPEP 3 GLY C 188 PRO C 189 0 0.33 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