HEADER PROTEIN FIBRIL 20-JUN-17 5W7V TITLE CRYOEM STRUCTURE OF THE SEGMENT, DLIIKGISVHI, ASSEMBLED INTO A TRIPLE- TITLE 2 HELICAL FIBRIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR DNA-BINDING PROTEIN 43; COMPND 3 CHAIN: 1, 3, 2, 6, 5, 4, 7, 0, 8; COMPND 4 FRAGMENT: RRM2 PEPTIDE (UNP RESIDUES 247-257); COMPND 5 SYNONYM: TDP-43, DLIIKGISVHI; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID, STERIC ZIPPER, PROTEIN FIBRIL EXPDTA ELECTRON MICROSCOPY AUTHOR E.L.GUENTHER,P.GE,D.S.EISENBERG REVDAT 6 13-MAR-24 5W7V 1 REMARK REVDAT 5 01-JAN-20 5W7V 1 REMARK REVDAT 4 18-JUL-18 5W7V 1 REMARK REVDAT 3 18-APR-18 5W7V 1 JRNL REVDAT 2 28-MAR-18 5W7V 1 JRNL REVDAT 1 14-MAR-18 5W7V 0 JRNL AUTH E.L.GUENTHER,P.GE,H.TRINH,M.R.SAWAYA,D.CASCIO,D.R.BOYER, JRNL AUTH 2 T.GONEN,Z.H.ZHOU,D.S.EISENBERG JRNL TITL ATOMIC-LEVEL EVIDENCE FOR PACKING AND POSITIONAL AMYLOID JRNL TITL 2 POLYMORPHISM BY SEGMENT FROM TDP-43 RRM2. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 311 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29531287 JRNL DOI 10.1038/S41594-018-0045-5 REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EMAN, LEGINON, CTFFIND, RELION REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE 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 : 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) : 3.800 REMARK 3 NUMBER OF PARTICLES : 18818 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 5W7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228525. 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 : DLIIKGISVHI 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 : 7.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 610 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 QUANTUM (4K X 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 120.00 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 300 THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR REMARK 300 HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: REMARK 300 ROTATION PER SUBUNIT (TWIST) = -120.44 DEGREES REMARK 300 RISE PER SUBUNIT (HEIGHT) = 1.60 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 APPLY THE FOLLOWING TO CHAINS: 1, 3, 2, 6, 5, 4, 7, 0, 8 REMARK 350 BIOMT1 1 0.993343 -0.115197 0.000000 0.00000 REMARK 350 BIOMT2 1 0.115197 0.993343 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 -23.97000 REMARK 350 BIOMT1 2 -0.403960 0.914776 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.914776 -0.403960 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -22.37200 REMARK 350 BIOMT1 3 -0.584009 -0.811747 0.000000 0.00000 REMARK 350 BIOMT2 3 0.811747 -0.584009 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 -20.77400 REMARK 350 BIOMT1 4 0.995738 -0.092232 0.000000 0.00000 REMARK 350 BIOMT2 4 0.092232 0.995738 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 -19.17600 REMARK 350 BIOMT1 5 -0.424974 0.905206 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.905206 -0.424974 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 -17.57800 REMARK 350 BIOMT1 6 -0.565111 -0.825015 0.000000 0.00000 REMARK 350 BIOMT2 6 0.825015 -0.565111 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -15.98000 REMARK 350 BIOMT1 7 0.997602 -0.069217 0.000000 0.00000 REMARK 350 BIOMT2 7 0.069217 0.997602 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -14.38200 REMARK 350 BIOMT1 8 -0.445760 0.895152 0.000000 0.00000 REMARK 350 BIOMT2 8 -0.895152 -0.445760 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -12.78400 REMARK 350 BIOMT1 9 -0.545912 -0.837843 0.000000 0.00000 REMARK 350 BIOMT2 9 0.837843 -0.545912 0.000000 0.00000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -11.18600 REMARK 350 BIOMT1 10 0.998934 -0.046165 0.000000 0.00000 REMARK 350 BIOMT2 10 0.046165 0.998934 0.000000 0.00000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -9.58800 REMARK 350 BIOMT1 11 -0.466309 0.884622 0.000000 0.00000 REMARK 350 BIOMT2 11 -0.884622 -0.466309 0.000000 0.00000 REMARK 350 BIOMT3 11 0.000000 0.000000 1.000000 -7.99000 REMARK 350 BIOMT1 12 -0.526422 -0.850224 0.000000 0.00000 REMARK 350 BIOMT2 12 0.850224 -0.526422 0.000000 0.00000 REMARK 350 BIOMT3 12 0.000000 0.000000 1.000000 -6.39200 REMARK 350 BIOMT1 13 0.999733 -0.023089 0.000000 0.00000 REMARK 350 BIOMT2 13 0.023089 0.999733 0.000000 0.00000 REMARK 350 BIOMT3 13 0.000000 0.000000 1.000000 -4.79400 REMARK 350 BIOMT1 14 -0.486610 0.873619 0.000000 0.00000 REMARK 350 BIOMT2 14 -0.873619 -0.486610 0.000000 0.00000 REMARK 350 BIOMT3 14 0.000000 0.000000 1.000000 -3.19600 REMARK 350 BIOMT1 15 -0.506651 -0.862151 0.000000 0.00000 REMARK 350 BIOMT2 15 0.862151 -0.506651 0.000000 0.00000 REMARK 350 BIOMT3 15 0.000000 0.000000 1.000000 -1.59800 REMARK 350 BIOMT1 16 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 16 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 16 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 17 -0.506651 0.862151 0.000000 0.00000 REMARK 350 BIOMT2 17 -0.862151 -0.506651 0.000000 0.00000 REMARK 350 BIOMT3 17 0.000000 0.000000 1.000000 1.59800 REMARK 350 BIOMT1 18 -0.486610 -0.873619 0.000000 0.00000 REMARK 350 BIOMT2 18 0.873619 -0.486610 0.000000 0.00000 REMARK 350 BIOMT3 18 0.000000 0.000000 1.000000 3.19600 REMARK 350 BIOMT1 19 0.999733 0.023089 0.000000 0.00000 REMARK 350 BIOMT2 19 -0.023089 0.999733 0.000000 0.00000 REMARK 350 BIOMT3 19 0.000000 0.000000 1.000000 4.79400 REMARK 350 BIOMT1 20 -0.526422 0.850224 0.000000 0.00000 REMARK 350 BIOMT2 20 -0.850224 -0.526422 0.000000 0.00000 REMARK 350 BIOMT3 20 0.000000 0.000000 1.000000 6.39200 REMARK 350 BIOMT1 21 -0.466309 -0.884622 0.000000 0.00000 REMARK 350 BIOMT2 21 0.884622 -0.466309 0.000000 0.00000 REMARK 350 BIOMT3 21 0.000000 0.000000 1.000000 7.99000 REMARK 350 BIOMT1 22 0.998934 0.046165 0.000000 0.00000 REMARK 350 BIOMT2 22 -0.046165 0.998934 0.000000 0.00000 REMARK 350 BIOMT3 22 0.000000 0.000000 1.000000 9.58800 REMARK 350 BIOMT1 23 -0.545912 0.837843 0.000000 0.00000 REMARK 350 BIOMT2 23 -0.837843 -0.545912 0.000000 0.00000 REMARK 350 BIOMT3 23 0.000000 0.000000 1.000000 11.18600 REMARK 350 BIOMT1 24 -0.445760 -0.895152 0.000000 0.00000 REMARK 350 BIOMT2 24 0.895152 -0.445760 0.000000 0.00000 REMARK 350 BIOMT3 24 0.000000 0.000000 1.000000 12.78400 REMARK 350 BIOMT1 25 0.997602 0.069217 0.000000 0.00000 REMARK 350 BIOMT2 25 -0.069217 0.997602 0.000000 0.00000 REMARK 350 BIOMT3 25 0.000000 0.000000 1.000000 14.38200 REMARK 350 BIOMT1 26 -0.565111 0.825015 0.000000 0.00000 REMARK 350 BIOMT2 26 -0.825015 -0.565111 0.000000 0.00000 REMARK 350 BIOMT3 26 0.000000 0.000000 1.000000 15.98000 REMARK 350 BIOMT1 27 -0.424974 -0.905206 0.000000 0.00000 REMARK 350 BIOMT2 27 0.905206 -0.424974 0.000000 0.00000 REMARK 350 BIOMT3 27 0.000000 0.000000 1.000000 17.57800 REMARK 350 BIOMT1 28 0.995738 0.092232 0.000000 0.00000 REMARK 350 BIOMT2 28 -0.092232 0.995738 0.000000 0.00000 REMARK 350 BIOMT3 28 0.000000 0.000000 1.000000 19.17600 REMARK 350 BIOMT1 29 -0.584009 0.811747 0.000000 0.00000 REMARK 350 BIOMT2 29 -0.811747 -0.584009 0.000000 0.00000 REMARK 350 BIOMT3 29 0.000000 0.000000 1.000000 20.77400 REMARK 350 BIOMT1 30 -0.403960 -0.914776 0.000000 0.00000 REMARK 350 BIOMT2 30 0.914776 -0.403960 0.000000 0.00000 REMARK 350 BIOMT3 30 0.000000 0.000000 1.000000 22.37200 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 0 7 REMARK 465 SER 0 8 REMARK 465 VAL 0 9 REMARK 465 HIS 0 10 REMARK 465 ILE 0 11 REMARK 465 GLY 8 6 REMARK 465 ILE 8 7 REMARK 465 SER 8 8 REMARK 465 VAL 8 9 REMARK 465 HIS 8 10 REMARK 465 ILE 8 11 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 ILE 4 7 -64.89 -101.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-8781 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF THE SEGMENT, DLIIKGISVHI, ASSEMBLED INTO A REMARK 900 TRIPLE-HELICAL FIBRIL DBREF 5W7V 1 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 3 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 2 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 6 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 5 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 4 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 7 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 0 1 11 UNP Q13148 TADBP_HUMAN 247 257 DBREF 5W7V 8 1 11 UNP Q13148 TADBP_HUMAN 247 257 SEQRES 1 1 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 3 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 2 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 6 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 5 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 4 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 7 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 0 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE SEQRES 1 8 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE 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