HEADER PROTEIN FIBRIL 02-DEC-20 7KWZ TITLE TDP-43 LCD AMYLOID FIBRILS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 2 OF TAR DNA-BINDING PROTEIN 43; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: TDP-43; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TARDBP, TDP43; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TDP-43, AMYLOID, NEURODEGENERATIVE DISEASES, AMYOTROPIC LATERAL KEYWDS 2 SCLEROSIS, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR Q.LI,W.M.BABINCHAK,W.K.SUREWICZ REVDAT 3 06-MAR-24 7KWZ 1 SHEET REVDAT 2 24-MAR-21 7KWZ 1 JRNL REVDAT 1 24-FEB-21 7KWZ 0 JRNL AUTH Q.LI,W.M.BABINCHAK,W.K.SUREWICZ JRNL TITL CRYO-EM STRUCTURE OF AMYLOID FIBRILS FORMED BY THE ENTIRE JRNL TITL 2 LOW COMPLEXITY DOMAIN OF TDP-43. JRNL REF NAT COMMUN V. 12 1620 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33712624 JRNL DOI 10.1038/S41467-021-21912-Y REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 11026 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 7KWZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253288. 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 FIBRILS FORMED BY TDP REMARK 245 -43 LOW COMPLEXITY DOMAIN 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 : 4.00 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) : 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 : OTHER REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4200.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -1.66 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 4.73 ANGSTROMS 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: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 ASN A 267 REMARK 465 ARG A 268 REMARK 465 GLN A 269 REMARK 465 LEU A 270 REMARK 465 GLU A 271 REMARK 465 ARG A 272 REMARK 465 SER A 273 REMARK 465 GLY A 274 REMARK 465 ARG A 275 REMARK 465 ASN B 267 REMARK 465 ARG B 268 REMARK 465 GLN B 269 REMARK 465 LEU B 270 REMARK 465 GLU B 271 REMARK 465 ARG B 272 REMARK 465 SER B 273 REMARK 465 GLY B 274 REMARK 465 ARG B 275 REMARK 465 ASN C 267 REMARK 465 ARG C 268 REMARK 465 GLN C 269 REMARK 465 LEU C 270 REMARK 465 GLU C 271 REMARK 465 ARG C 272 REMARK 465 SER C 273 REMARK 465 GLY C 274 REMARK 465 ARG C 275 REMARK 465 ASN D 267 REMARK 465 ARG D 268 REMARK 465 GLN D 269 REMARK 465 LEU D 270 REMARK 465 GLU D 271 REMARK 465 ARG D 272 REMARK 465 SER D 273 REMARK 465 GLY D 274 REMARK 465 ARG D 275 REMARK 465 ASN E 267 REMARK 465 ARG E 268 REMARK 465 GLN E 269 REMARK 465 LEU E 270 REMARK 465 GLU E 271 REMARK 465 ARG E 272 REMARK 465 SER E 273 REMARK 465 GLY E 274 REMARK 465 ARG E 275 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 ASN A 279 63.94 -160.25 REMARK 500 MET A 337 -57.49 -120.61 REMARK 500 MET A 339 118.78 -160.63 REMARK 500 GLN A 344 50.64 -97.72 REMARK 500 SER A 404 119.96 -162.31 REMARK 500 ASN B 279 63.92 -160.25 REMARK 500 MET B 337 -57.51 -120.65 REMARK 500 MET B 339 118.78 -160.63 REMARK 500 GLN B 344 50.64 -97.73 REMARK 500 SER B 404 119.92 -162.31 REMARK 500 ASN C 279 63.93 -160.30 REMARK 500 MET C 337 -57.47 -120.57 REMARK 500 MET C 339 118.74 -160.67 REMARK 500 GLN C 344 50.65 -97.71 REMARK 500 SER C 404 119.96 -162.27 REMARK 500 ASN D 279 63.97 -160.23 REMARK 500 MET D 337 -57.47 -120.61 REMARK 500 MET D 339 118.83 -160.64 REMARK 500 GLN D 344 50.72 -97.76 REMARK 500 SER D 404 119.95 -162.28 REMARK 500 ASN E 279 63.93 -160.30 REMARK 500 MET E 337 -57.48 -120.65 REMARK 500 MET E 339 118.76 -160.69 REMARK 500 GLN E 344 50.70 -97.78 REMARK 500 SER E 404 119.99 -162.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-23059 RELATED DB: EMDB REMARK 900 TDP-43 LCD AMYLOID FIBRILS DBREF 7KWZ A 267 414 UNP Q13148 TADBP_HUMAN 151 298 DBREF 7KWZ B 267 414 UNP Q13148 TADBP_HUMAN 151 298 DBREF 7KWZ C 267 414 UNP Q13148 TADBP_HUMAN 151 298 DBREF 7KWZ D 267 414 UNP Q13148 TADBP_HUMAN 151 298 DBREF 7KWZ E 267 414 UNP Q13148 TADBP_HUMAN 151 298 SEQRES 1 A 148 ASN ARG GLN LEU GLU ARG SER GLY ARG PHE GLY GLY ASN SEQRES 2 A 148 PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SER SEQRES 3 A 148 ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SER SEQRES 4 A 148 ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER ILE SEQRES 5 A 148 ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU GLN SEQRES 6 A 148 SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN GLN SEQRES 7 A 148 ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN GLY SEQRES 8 A 148 ASN MET GLN ARG GLU PRO ASN GLN ALA PHE GLY SER GLY SEQRES 9 A 148 ASN ASN SER TYR SER GLY SER ASN SER GLY ALA ALA ILE SEQRES 10 A 148 GLY TRP GLY SER ALA SER ASN ALA GLY SER GLY SER GLY SEQRES 11 A 148 PHE ASN GLY GLY PHE GLY SER SER MET ASP SER LYS SER SEQRES 12 A 148 SER GLY TRP GLY MET SEQRES 1 B 148 ASN ARG GLN LEU GLU ARG SER GLY ARG PHE GLY GLY ASN SEQRES 2 B 148 PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SER SEQRES 3 B 148 ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SER SEQRES 4 B 148 ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER ILE SEQRES 5 B 148 ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU GLN SEQRES 6 B 148 SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN GLN SEQRES 7 B 148 ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN GLY SEQRES 8 B 148 ASN MET GLN ARG GLU PRO ASN GLN ALA PHE GLY SER GLY SEQRES 9 B 148 ASN ASN SER TYR SER GLY SER ASN SER GLY ALA ALA ILE SEQRES 10 B 148 GLY TRP GLY SER ALA SER ASN ALA GLY SER GLY SER GLY SEQRES 11 B 148 PHE ASN GLY GLY PHE GLY SER SER MET ASP SER LYS SER SEQRES 12 B 148 SER GLY TRP GLY MET SEQRES 1 C 148 ASN ARG GLN LEU GLU ARG SER GLY ARG PHE GLY GLY ASN SEQRES 2 C 148 PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SER SEQRES 3 C 148 ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SER SEQRES 4 C 148 ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER ILE SEQRES 5 C 148 ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU GLN SEQRES 6 C 148 SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN GLN SEQRES 7 C 148 ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN GLY SEQRES 8 C 148 ASN MET GLN ARG GLU PRO ASN GLN ALA PHE GLY SER GLY SEQRES 9 C 148 ASN ASN SER TYR SER GLY SER ASN SER GLY ALA ALA ILE SEQRES 10 C 148 GLY TRP GLY SER ALA SER ASN ALA GLY SER GLY SER GLY SEQRES 11 C 148 PHE ASN GLY GLY PHE GLY SER SER MET ASP SER LYS SER SEQRES 12 C 148 SER GLY TRP GLY MET SEQRES 1 D 148 ASN ARG GLN LEU GLU ARG SER GLY ARG PHE GLY GLY ASN SEQRES 2 D 148 PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SER SEQRES 3 D 148 ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SER SEQRES 4 D 148 ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER ILE SEQRES 5 D 148 ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU GLN SEQRES 6 D 148 SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN GLN SEQRES 7 D 148 ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN GLY SEQRES 8 D 148 ASN MET GLN ARG GLU PRO ASN GLN ALA PHE GLY SER GLY SEQRES 9 D 148 ASN ASN SER TYR SER GLY SER ASN SER GLY ALA ALA ILE SEQRES 10 D 148 GLY TRP GLY SER ALA SER ASN ALA GLY SER GLY SER GLY SEQRES 11 D 148 PHE ASN GLY GLY PHE GLY SER SER MET ASP SER LYS SER SEQRES 12 D 148 SER GLY TRP GLY MET SEQRES 1 E 148 ASN ARG GLN LEU GLU ARG SER GLY ARG PHE GLY GLY ASN SEQRES 2 E 148 PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SER SEQRES 3 E 148 ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SER SEQRES 4 E 148 ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER ILE SEQRES 5 E 148 ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU GLN SEQRES 6 E 148 SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN GLN SEQRES 7 E 148 ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN GLY SEQRES 8 E 148 ASN MET GLN ARG GLU PRO ASN GLN ALA PHE GLY SER GLY SEQRES 9 E 148 ASN ASN SER TYR SER GLY SER ASN SER GLY ALA ALA ILE SEQRES 10 E 148 GLY TRP GLY SER ALA SER ASN ALA GLY SER GLY SER GLY SEQRES 11 E 148 PHE ASN GLY GLY PHE GLY SER SER MET ASP SER LYS SER SEQRES 12 E 148 SER GLY TRP GLY MET SHEET 1 170 MET E 311 PHE E 313 0 SHEET 2 170 MET D 311 PHE D 313 1 SHEET 3 170 MET C 311 PHE C 313 1 SHEET 4 170 MET B 311 PHE B 313 1 SHEET 5 170 MET A 311 PHE A 313 1 SHEET 6 170 MET E 322 ALA E 325 0 SHEET 7 170 MET D 322 ALA D 325 1 SHEET 8 170 MET C 322 ALA C 325 1 SHEET 9 170 MET B 322 ALA B 325 1 SHEET 10 170 MET A 322 ALA A 325 1 SHEET 11 170 ALA E 328 LEU E 330 0 SHEET 12 170 ALA D 328 LEU D 330 1 SHEET 13 170 ALA C 328 LEU C 330 1 SHEET 14 170 ALA B 328 LEU B 330 1 SHEET 15 170 ALA A 328 LEU A 330 1 SHEET 16 170 ALA E 341 GLN E 343 0 SHEET 17 170 ALA D 341 GLN D 343 1 SHEET 18 170 ALA C 341 GLN C 343 1 SHEET 19 170 ALA B 341 GLN B 343 1 SHEET 20 170 ALA A 341 GLN A 343 1 SHEET 21 170 ASN E 352 ASN E 355 0 SHEET 22 170 ASN D 352 ASN D 355 1 SHEET 23 170 ASN C 352 ASN C 355 1 SHEET 24 170 ASN B 352 ASN B 355 1 SHEET 25 170 ASN A 352 ASN A 355 1 SHEET 26 170 ASN E 372 ASN E 378 0 SHEET 27 170 ASN D 372 ASN D 378 1 SHEET 28 170 ASN C 372 ASN C 378 1 SHEET 29 170 ASN B 372 ASN B 378 1 SHEET 30 170 ASN A 372 ASN A 378 1 SHEET 31 170 ALA E 382 GLY E 384 0 SHEET 32 170 ALA D 382 GLY D 384 1 SHEET 33 170 ALA B 382 GLY B 384 1 SHEET 34 170 ALA A 382 GLY A 384 1 SHEET 35 170 ALA C 382 GLY C 384 1 SHEET 36 170 ALA E 388 GLY E 394 0 SHEET 37 170 ALA D 388 GLY D 394 1 SHEET 38 170 ALA C 388 GLY C 394 1 SHEET 39 170 ALA B 388 GLY B 394 1 SHEET 40 170 ALA A 388 GLY A 394 1 SHEET 41 170 SER E 404 GLY E 411 0 SHEET 42 170 SER D 404 GLY D 411 1 SHEET 43 170 SER C 404 GLY C 411 1 SHEET 44 170 SER B 404 GLY B 411 1 SHEET 45 170 SER A 404 GLY A 411 1 SHEET 46 170 PHE E 283 ASN E 285 0 SHEET 47 170 PHE D 283 ASN D 285 1 SHEET 48 170 PHE C 283 ASN C 285 1 SHEET 49 170 PHE B 283 ASN B 285 1 SHEET 50 170 PHE A 283 ASN A 285 1 SHEET 51 170 ASN E 301 ASN E 306 0 SHEET 52 170 ASN D 301 ASN D 306 1 SHEET 53 170 ASN C 301 ASN C 306 1 SHEET 54 170 ASN B 301 ASN B 306 1 SHEET 55 170 ASN A 301 ASN A 306 1 SHEET 56 170 PHE E 316 ILE E 318 0 SHEET 57 170 PHE D 316 ILE D 318 1 SHEET 58 170 PHE C 316 ILE C 318 1 SHEET 59 170 PHE B 316 ILE B 318 1 SHEET 60 170 PHE A 316 ILE A 318 1 SHEET 61 170 SER E 332 TRP E 334 0 SHEET 62 170 SER D 332 TRP D 334 1 SHEET 63 170 SER C 332 TRP C 334 1 SHEET 64 170 SER B 332 TRP B 334 1 SHEET 65 170 SER A 332 TRP A 334 1 SHEET 66 170 GLN E 346 GLY E 348 0 SHEET 67 170 GLN D 346 GLY D 348 1 SHEET 68 170 GLN C 346 GLY C 348 1 SHEET 69 170 GLN B 346 GLY B 348 1 SHEET 70 170 GLN A 346 GLY A 348 1 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