HEADER PROTEIN FIBRIL 28-JUL-22 7YMN TITLE CRYO-EM STRUCTURE OF IN VITRO PHF FIBRIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM TAU-D OF MICROTUBULE-ASSOCIATED PROTEIN TAU; COMPND 3 CHAIN: F, C, D, E, A, B; COMPND 4 SYNONYM: NEUROFIBRILLARY TANGLE PROTEIN,PAIRED HELICAL FILAMENT-TAU, COMPND 5 PHF-TAU; COMPND 6 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: MAPT, MAPTL, MTBT1, TAU; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS PROTEIN FIBRIL, AMYLOID EXPDTA ELECTRON MICROSCOPY AUTHOR X.LI,C.LIU REVDAT 3 03-JUL-24 7YMN 1 REMARK REVDAT 2 28-DEC-22 7YMN 1 JRNL REVDAT 1 14-DEC-22 7YMN 0 JRNL AUTH X.LI,S.ZHANG,Z.LIU,Y.TAO,W.XIA,Y.SUN,C.LIU,W.LE,B.SUN,D.LI JRNL TITL SUBTLE CHANGE OF FIBRILLATION CONDITION LEADS TO SUBSTANTIAL JRNL TITL 2 ALTERATION OF RECOMBINANT TAU FIBRIL STRUCTURE. JRNL REF ISCIENCE V. 25 05645 2022 JRNL REFN ESSN 2589-0042 JRNL PMID 36505939 JRNL DOI 10.1016/J.ISCI.2022.105645 REMARK 2 REMARK 2 RESOLUTION. 3.46 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) : 3.460 REMARK 3 NUMBER OF PARTICLES : 92332 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 7YMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031265. 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 : CRYO-EM STRUCTURE OF IN VITRO REMARK 245 PHF FIBRIL 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, C, D, E, A, B 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 ILE F 297 REMARK 465 LYS F 298 REMARK 465 HIS F 299 REMARK 465 VAL F 300 REMARK 465 PRO F 301 REMARK 465 GLY F 302 REMARK 465 GLY F 303 REMARK 465 GLU F 380 REMARK 465 ASN F 381 REMARK 465 ALA F 382 REMARK 465 LYS F 383 REMARK 465 ALA F 384 REMARK 465 LYS F 385 REMARK 465 THR F 386 REMARK 465 ASP F 387 REMARK 465 HIS F 388 REMARK 465 GLY F 389 REMARK 465 ALA F 390 REMARK 465 GLU F 391 REMARK 465 ILE C 297 REMARK 465 LYS C 298 REMARK 465 HIS C 299 REMARK 465 VAL C 300 REMARK 465 PRO C 301 REMARK 465 GLY C 302 REMARK 465 GLY C 303 REMARK 465 GLU C 380 REMARK 465 ASN C 381 REMARK 465 ALA C 382 REMARK 465 LYS C 383 REMARK 465 ALA C 384 REMARK 465 LYS C 385 REMARK 465 THR C 386 REMARK 465 ASP C 387 REMARK 465 HIS C 388 REMARK 465 GLY C 389 REMARK 465 ALA C 390 REMARK 465 GLU C 391 REMARK 465 ILE D 297 REMARK 465 LYS D 298 REMARK 465 HIS D 299 REMARK 465 VAL D 300 REMARK 465 PRO D 301 REMARK 465 GLY D 302 REMARK 465 GLY D 303 REMARK 465 GLU D 380 REMARK 465 ASN D 381 REMARK 465 ALA D 382 REMARK 465 LYS D 383 REMARK 465 ALA D 384 REMARK 465 LYS D 385 REMARK 465 THR D 386 REMARK 465 ASP D 387 REMARK 465 HIS D 388 REMARK 465 GLY D 389 REMARK 465 ALA D 390 REMARK 465 GLU D 391 REMARK 465 ILE E 297 REMARK 465 LYS E 298 REMARK 465 HIS E 299 REMARK 465 VAL E 300 REMARK 465 PRO E 301 REMARK 465 GLY E 302 REMARK 465 GLY E 303 REMARK 465 GLU E 380 REMARK 465 ASN E 381 REMARK 465 ALA E 382 REMARK 465 LYS E 383 REMARK 465 ALA E 384 REMARK 465 LYS E 385 REMARK 465 THR E 386 REMARK 465 ASP E 387 REMARK 465 HIS E 388 REMARK 465 GLY E 389 REMARK 465 ALA E 390 REMARK 465 GLU E 391 REMARK 465 ILE A 297 REMARK 465 LYS A 298 REMARK 465 HIS A 299 REMARK 465 VAL A 300 REMARK 465 PRO A 301 REMARK 465 GLY A 302 REMARK 465 GLY A 303 REMARK 465 GLU A 380 REMARK 465 ASN A 381 REMARK 465 ALA A 382 REMARK 465 LYS A 383 REMARK 465 ALA A 384 REMARK 465 LYS A 385 REMARK 465 THR A 386 REMARK 465 ASP A 387 REMARK 465 HIS A 388 REMARK 465 GLY A 389 REMARK 465 ALA A 390 REMARK 465 GLU A 391 REMARK 465 ILE B 297 REMARK 465 LYS B 298 REMARK 465 HIS B 299 REMARK 465 VAL B 300 REMARK 465 PRO B 301 REMARK 465 GLY B 302 REMARK 465 GLY B 303 REMARK 465 GLU B 380 REMARK 465 ASN B 381 REMARK 465 ALA B 382 REMARK 465 LYS B 383 REMARK 465 ALA B 384 REMARK 465 LYS B 385 REMARK 465 THR B 386 REMARK 465 ASP B 387 REMARK 465 HIS B 388 REMARK 465 GLY B 389 REMARK 465 ALA B 390 REMARK 465 GLU B 391 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 LYS F 311 79.21 -160.30 REMARK 500 SER F 324 134.33 -170.27 REMARK 500 ARG F 349 21.58 49.73 REMARK 500 LYS F 375 139.59 -170.29 REMARK 500 LYS C 311 79.27 -160.32 REMARK 500 SER C 324 134.32 -170.27 REMARK 500 ARG C 349 21.70 49.63 REMARK 500 LYS C 375 139.58 -170.35 REMARK 500 LYS D 311 79.33 -160.38 REMARK 500 SER D 324 134.28 -170.35 REMARK 500 ARG D 349 21.70 49.65 REMARK 500 LYS D 375 139.53 -170.35 REMARK 500 LYS E 311 79.23 -160.35 REMARK 500 SER E 324 134.33 -170.33 REMARK 500 ARG E 349 21.63 49.69 REMARK 500 LYS E 375 139.55 -170.39 REMARK 500 LYS A 311 79.31 -160.38 REMARK 500 SER A 324 134.40 -170.29 REMARK 500 ARG A 349 21.68 49.58 REMARK 500 LYS A 375 139.53 -170.39 REMARK 500 LYS B 311 79.31 -160.37 REMARK 500 SER B 324 134.33 -170.29 REMARK 500 ARG B 349 21.63 49.63 REMARK 500 LYS B 375 139.57 -170.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-33934 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF IN VITRO PHF FIBRIL DBREF 7YMN F 297 391 UNP P10636 TAU_HUMAN 239 333 DBREF 7YMN C 297 391 UNP P10636 TAU_HUMAN 239 333 DBREF 7YMN D 297 391 UNP P10636 TAU_HUMAN 239 333 DBREF 7YMN E 297 391 UNP P10636 TAU_HUMAN 239 333 DBREF 7YMN A 297 391 UNP P10636 TAU_HUMAN 239 333 DBREF 7YMN B 297 391 UNP P10636 TAU_HUMAN 239 333 SEQRES 1 F 95 ILE LYS HIS VAL PRO GLY GLY GLY SER VAL GLN ILE VAL SEQRES 2 F 95 TYR LYS PRO VAL ASP LEU SER LYS VAL THR SER LYS CYS SEQRES 3 F 95 GLY SER LEU GLY ASN ILE HIS HIS LYS PRO GLY GLY GLY SEQRES 4 F 95 GLN VAL GLU VAL LYS SER GLU LYS LEU ASP PHE LYS ASP SEQRES 5 F 95 ARG VAL GLN SER LYS ILE GLY SER LEU ASP ASN ILE THR SEQRES 6 F 95 HIS VAL PRO GLY GLY GLY ASN LYS LYS ILE GLU THR HIS SEQRES 7 F 95 LYS LEU THR PHE ARG GLU ASN ALA LYS ALA LYS THR ASP SEQRES 8 F 95 HIS GLY ALA GLU SEQRES 1 C 95 ILE LYS HIS VAL PRO GLY GLY GLY SER VAL GLN ILE VAL SEQRES 2 C 95 TYR LYS PRO VAL ASP LEU SER LYS VAL THR SER LYS CYS SEQRES 3 C 95 GLY SER LEU GLY ASN ILE HIS HIS LYS PRO GLY GLY GLY SEQRES 4 C 95 GLN VAL GLU VAL LYS SER GLU LYS LEU ASP PHE LYS ASP SEQRES 5 C 95 ARG VAL GLN SER LYS ILE GLY SER LEU ASP ASN ILE THR SEQRES 6 C 95 HIS VAL PRO GLY GLY GLY ASN LYS LYS ILE GLU THR HIS SEQRES 7 C 95 LYS LEU THR PHE ARG GLU ASN ALA LYS ALA LYS THR ASP SEQRES 8 C 95 HIS GLY ALA GLU SEQRES 1 D 95 ILE LYS HIS VAL PRO GLY GLY GLY SER VAL GLN ILE VAL SEQRES 2 D 95 TYR LYS PRO VAL ASP LEU SER LYS VAL THR SER LYS CYS SEQRES 3 D 95 GLY SER LEU GLY ASN ILE HIS HIS LYS PRO GLY GLY GLY SEQRES 4 D 95 GLN VAL GLU VAL LYS SER GLU LYS LEU ASP PHE LYS ASP SEQRES 5 D 95 ARG VAL GLN SER LYS ILE GLY SER LEU ASP ASN ILE THR SEQRES 6 D 95 HIS VAL PRO GLY GLY GLY ASN LYS LYS ILE GLU THR HIS SEQRES 7 D 95 LYS LEU THR PHE ARG GLU ASN ALA LYS ALA LYS THR ASP SEQRES 8 D 95 HIS GLY ALA GLU SEQRES 1 E 95 ILE LYS HIS VAL PRO GLY GLY GLY SER VAL GLN ILE VAL SEQRES 2 E 95 TYR LYS PRO VAL ASP LEU SER LYS VAL THR SER LYS CYS SEQRES 3 E 95 GLY SER LEU GLY ASN ILE HIS HIS LYS PRO GLY GLY GLY SEQRES 4 E 95 GLN VAL GLU VAL LYS SER GLU LYS LEU ASP PHE LYS ASP SEQRES 5 E 95 ARG VAL GLN SER LYS ILE GLY SER LEU ASP ASN ILE THR SEQRES 6 E 95 HIS VAL PRO GLY GLY GLY ASN LYS LYS ILE GLU THR HIS SEQRES 7 E 95 LYS LEU THR PHE ARG GLU ASN ALA LYS ALA LYS THR ASP SEQRES 8 E 95 HIS GLY ALA GLU SEQRES 1 A 95 ILE LYS HIS VAL PRO GLY GLY GLY SER VAL GLN ILE VAL SEQRES 2 A 95 TYR LYS PRO VAL ASP LEU SER LYS VAL THR SER LYS CYS SEQRES 3 A 95 GLY SER LEU GLY ASN ILE HIS HIS LYS PRO GLY GLY GLY SEQRES 4 A 95 GLN VAL GLU VAL LYS SER GLU LYS LEU ASP PHE LYS ASP SEQRES 5 A 95 ARG VAL GLN SER LYS ILE GLY SER LEU ASP ASN ILE THR SEQRES 6 A 95 HIS VAL PRO GLY GLY GLY ASN LYS LYS ILE GLU THR HIS SEQRES 7 A 95 LYS LEU THR PHE ARG GLU ASN ALA LYS ALA LYS THR ASP SEQRES 8 A 95 HIS GLY ALA GLU SEQRES 1 B 95 ILE LYS HIS VAL PRO GLY GLY GLY SER VAL GLN ILE VAL SEQRES 2 B 95 TYR LYS PRO VAL ASP LEU SER LYS VAL THR SER LYS CYS SEQRES 3 B 95 GLY SER LEU GLY ASN ILE HIS HIS LYS PRO GLY GLY GLY SEQRES 4 B 95 GLN VAL GLU VAL LYS SER GLU LYS LEU ASP PHE LYS ASP SEQRES 5 B 95 ARG VAL GLN SER LYS ILE GLY SER LEU ASP ASN ILE THR SEQRES 6 B 95 HIS VAL PRO GLY GLY GLY ASN LYS LYS ILE GLU THR HIS SEQRES 7 B 95 LYS LEU THR PHE ARG GLU ASN ALA LYS ALA LYS THR ASP SEQRES 8 B 95 HIS GLY ALA GLU SHEET 1 AA1 3 GLN C 307 ILE C 308 0 SHEET 2 AA1 3 GLN F 307 ILE F 308 1 N GLN F 307 O ILE C 308 SHEET 3 AA1 3 GLN D 307 ILE D 308 1 O GLN D 307 N ILE F 308 SHEET 1 AA2 3 LEU C 325 ILE C 328 0 SHEET 2 AA2 3 LEU F 325 ILE F 328 1 N GLY F 326 O LEU C 325 SHEET 3 AA2 3 LEU D 325 ILE D 328 1 O GLY D 326 N LEU F 325 SHEET 1 AA3 3 LYS C 343 LEU C 344 0 SHEET 2 AA3 3 LYS F 343 LEU F 344 1 N LYS F 343 O LEU C 344 SHEET 3 AA3 3 LYS D 343 LEU D 344 1 O LYS D 343 N LEU F 344 SHEET 1 AA4 3 ASP C 358 ASN C 359 0 SHEET 2 AA4 3 ASP F 358 ASN F 359 1 N ASP F 358 O ASN C 359 SHEET 3 AA4 3 ASP D 358 ASN D 359 1 O ASP D 358 N ASN F 359 SHEET 1 AA5 3 GLN A 307 ILE A 308 0 SHEET 2 AA5 3 GLN E 307 ILE E 308 1 N GLN E 307 O ILE A 308 SHEET 3 AA5 3 GLN B 307 ILE B 308 1 O GLN B 307 N ILE E 308 SHEET 1 AA6 3 LEU A 325 ILE A 328 0 SHEET 2 AA6 3 LEU E 325 ILE E 328 1 N GLY E 326 O LEU A 325 SHEET 3 AA6 3 LEU B 325 ILE B 328 1 O GLY B 326 N LEU E 325 SHEET 1 AA7 3 LYS A 343 LEU A 344 0 SHEET 2 AA7 3 LYS E 343 LEU E 344 1 N LYS E 343 O LEU A 344 SHEET 3 AA7 3 LYS B 343 LEU B 344 1 O LYS B 343 N LEU E 344 SHEET 1 AA8 3 ASP A 358 ASN A 359 0 SHEET 2 AA8 3 ASP E 358 ASN E 359 1 N ASP E 358 O ASN A 359 SHEET 3 AA8 3 ASP B 358 ASN B 359 1 O ASP B 358 N ASN E 359 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