HEADER RNA BINDING PROTEIN 28-OCT-21 7Q3U TITLE CRYO-EM STRUCTURE OF TDP43 CORE PEPTIDE AMYLOID FIBER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR DNA-BINDING PROTEIN 43; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 SYNONYM: TDP-43; 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: TARDBP, TDP43; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TDP-43, AMYLOID, NEURODEGENERATION, HELICAL, CRYO-EM, RNA BINDING KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.NAZAROV REVDAT 3 04-OCT-23 7Q3U 1 JRNL REVDAT 2 12-APR-23 7Q3U 1 REMARK REVDAT 1 22-MAR-23 7Q3U 0 JRNL AUTH S.T.KUMAR,S.NAZAROV,S.PORTA,N.MAHARJAN,U.CENDROWSKA, JRNL AUTH 2 M.KABANI,F.FINAMORE,Y.XU,V.M.LEE,H.A.LASHUEL JRNL TITL SEEDING THE AGGREGATION OF TDP-43 REQUIRES JRNL TITL 2 POST-FIBRILLIZATION PROTEOLYTIC CLEAVAGE. JRNL REF NAT.NEUROSCI. V. 26 983 2023 JRNL REFN ISSN 1097-6256 JRNL PMID 37248338 JRNL DOI 10.1038/S41593-023-01341-4 REMARK 2 REMARK 2 RESOLUTION. 3.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, COOT, RELION, RELION, RELION, REMARK 3 RELION, PHENIX 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 : 103.000 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) : 3.700 REMARK 3 NUMBER OF PARTICLES : 5795 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 7Q3U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292118470. 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 : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : HELICAL FILAMENT FROM TDP43 REMARK 245 CORE PEPTIDE 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 : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 3171 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) : 900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 81000 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 21040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL 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 279 REMARK 465 PRO A 280 REMARK 465 ASN A 352 REMARK 465 ASN A 353 REMARK 465 GLN A 354 REMARK 465 ASN A 355 REMARK 465 GLN A 356 REMARK 465 GLY A 357 REMARK 465 ASN A 358 REMARK 465 MET A 359 REMARK 465 GLN A 360 REMARK 465 ASN B 279 REMARK 465 PRO B 280 REMARK 465 ASN B 352 REMARK 465 ASN B 353 REMARK 465 GLN B 354 REMARK 465 ASN B 355 REMARK 465 GLN B 356 REMARK 465 GLY B 357 REMARK 465 ASN B 358 REMARK 465 MET B 359 REMARK 465 GLN B 360 REMARK 465 ASN C 279 REMARK 465 PRO C 280 REMARK 465 ASN C 352 REMARK 465 ASN C 353 REMARK 465 GLN C 354 REMARK 465 ASN C 355 REMARK 465 GLN C 356 REMARK 465 GLY C 357 REMARK 465 ASN C 358 REMARK 465 MET C 359 REMARK 465 GLN C 360 REMARK 465 ASN D 279 REMARK 465 PRO D 280 REMARK 465 ASN D 352 REMARK 465 ASN D 353 REMARK 465 GLN D 354 REMARK 465 ASN D 355 REMARK 465 GLN D 356 REMARK 465 GLY D 357 REMARK 465 ASN D 358 REMARK 465 MET D 359 REMARK 465 GLN D 360 REMARK 465 ASN E 279 REMARK 465 PRO E 280 REMARK 465 ASN E 352 REMARK 465 ASN E 353 REMARK 465 GLN E 354 REMARK 465 ASN E 355 REMARK 465 GLN E 356 REMARK 465 GLY E 357 REMARK 465 ASN E 358 REMARK 465 MET E 359 REMARK 465 GLN E 360 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 NE2 GLN A 331 OG SER D 347 2.12 REMARK 500 OG SER B 347 NE2 GLN C 331 2.16 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 ASN A 291 -129.02 57.44 REMARK 500 ALA A 326 -137.79 58.92 REMARK 500 GLN A 344 114.73 -162.32 REMARK 500 ASN B 291 -129.06 57.41 REMARK 500 ALA B 326 -137.75 58.91 REMARK 500 GLN B 344 114.66 -162.43 REMARK 500 ASN C 291 -128.99 57.37 REMARK 500 ALA C 326 -137.74 58.96 REMARK 500 GLN C 344 114.70 -162.34 REMARK 500 ASN D 291 -128.97 57.42 REMARK 500 ALA D 326 -137.76 58.93 REMARK 500 GLN D 344 114.70 -162.41 REMARK 500 ASN E 291 -129.01 57.39 REMARK 500 ALA E 326 -137.77 58.86 REMARK 500 GLN E 344 114.74 -162.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-13795 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF TDP43 CORE PEPTIDE AMYLOID FIBER DBREF 7Q3U A 279 360 UNP Q13148 TADBP_HUMAN 279 360 DBREF 7Q3U B 279 360 UNP Q13148 TADBP_HUMAN 279 360 DBREF 7Q3U C 279 360 UNP Q13148 TADBP_HUMAN 279 360 DBREF 7Q3U D 279 360 UNP Q13148 TADBP_HUMAN 279 360 DBREF 7Q3U E 279 360 UNP Q13148 TADBP_HUMAN 279 360 SEQRES 1 A 82 ASN PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SEQRES 2 A 82 SER ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SEQRES 3 A 82 SER ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER SEQRES 4 A 82 ILE ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU SEQRES 5 A 82 GLN SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN SEQRES 6 A 82 GLN ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN SEQRES 7 A 82 GLY ASN MET GLN SEQRES 1 B 82 ASN PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SEQRES 2 B 82 SER ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SEQRES 3 B 82 SER ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER SEQRES 4 B 82 ILE ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU SEQRES 5 B 82 GLN SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN SEQRES 6 B 82 GLN ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN SEQRES 7 B 82 GLY ASN MET GLN SEQRES 1 C 82 ASN PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SEQRES 2 C 82 SER ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SEQRES 3 C 82 SER ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER SEQRES 4 C 82 ILE ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU SEQRES 5 C 82 GLN SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN SEQRES 6 C 82 GLN ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN SEQRES 7 C 82 GLY ASN MET GLN SEQRES 1 D 82 ASN PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SEQRES 2 D 82 SER ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SEQRES 3 D 82 SER ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER SEQRES 4 D 82 ILE ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU SEQRES 5 D 82 GLN SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN SEQRES 6 D 82 GLN ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN SEQRES 7 D 82 GLY ASN MET GLN SEQRES 1 E 82 ASN PRO GLY GLY PHE GLY ASN GLN GLY GLY PHE GLY ASN SEQRES 2 E 82 SER ARG GLY GLY GLY ALA GLY LEU GLY ASN ASN GLN GLY SEQRES 3 E 82 SER ASN MET GLY GLY GLY MET ASN PHE GLY ALA PHE SER SEQRES 4 E 82 ILE ASN PRO ALA MET MET ALA ALA ALA GLN ALA ALA LEU SEQRES 5 E 82 GLN SER SER TRP GLY MET MET GLY MET LEU ALA SER GLN SEQRES 6 E 82 GLN ASN GLN SER GLY PRO SER GLY ASN ASN GLN ASN GLN SEQRES 7 E 82 GLY ASN MET GLN SHEET 1 AA1 5 MET C 311 ASN C 312 0 SHEET 2 AA1 5 MET A 311 ASN A 312 1 N ASN A 312 O MET C 311 SHEET 3 AA1 5 GLY B 310 ASN B 312 1 O GLY B 310 N MET A 311 SHEET 4 AA1 5 GLY D 310 ASN D 312 1 O GLY D 310 N MET B 311 SHEET 5 AA1 5 GLY E 310 ASN E 312 1 O GLY E 310 N MET D 311 SHEET 1 AA2 5 SER C 317 ILE C 318 0 SHEET 2 AA2 5 SER A 317 ILE A 318 1 N ILE A 318 O SER C 317 SHEET 3 AA2 5 SER B 317 ILE B 318 1 O ILE B 318 N SER A 317 SHEET 4 AA2 5 SER D 317 ILE D 318 1 O ILE D 318 N SER B 317 SHEET 5 AA2 5 SER E 317 ILE E 318 1 O ILE E 318 N SER D 317 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 TER 472 GLY A 351 TER 944 GLY B 351 TER 1416 GLY C 351 TER 1888 GLY D 351 TER 2360 GLY E 351 MASTER 209 0 0 0 10 0 0 6 2355 5 0 35 END