HEADER PROTEIN FIBRIL 15-FEB-18 6CFH TITLE SWGMMGMLASQ SEGMENT FROM THE LOW COMPLEXITY DOMAIN OF TDP-43 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR DNA-BINDING PROTEIN 43; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SWGMMGMLASQ SEGMENT; COMPND 5 SYNONYM: TDP-43; 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; SOURCE 6 OTHER_DETAILS: SYNTHETIC PEPTIDE SWGMMGMLASQ CORRESPONDING TOSEGMENT SOURCE 7 333-343 OF TDP-43 KEYWDS AMYLOID, STERIC ZIPPER, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR E.L.GUENTHER,J.A.RODRIGUEZ,M.R.SAWAYA,D.S.EISENBERG REVDAT 8 15-MAY-24 6CFH 1 REMARK REVDAT 7 13-OCT-21 6CFH 1 REMARK REVDAT 6 30-JUN-21 6CFH 1 REMARK REVDAT 5 17-JUN-20 6CFH 1 COMPND SOURCE DBREF REVDAT 4 18-DEC-19 6CFH 1 REMARK REVDAT 3 13-JUN-18 6CFH 1 JRNL REVDAT 2 06-JUN-18 6CFH 1 JRNL REVDAT 1 23-MAY-18 6CFH 0 JRNL AUTH E.L.GUENTHER,Q.CAO,H.TRINH,J.LU,M.R.SAWAYA,D.CASCIO, JRNL AUTH 2 D.R.BOYER,J.A.RODRIGUEZ,M.P.HUGHES,D.S.EISENBERG JRNL TITL ATOMIC STRUCTURES OF TDP-43 LCD SEGMENTS AND INSIGHTS INTO JRNL TITL 2 REVERSIBLE OR PATHOGENIC AGGREGATION. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 463 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29786080 JRNL DOI 10.1038/S41594-018-0064-2 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 1819 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.283 REMARK 3 R VALUE (WORKING SET) : 0.280 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 182 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.32 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 510 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2199 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 459 REMARK 3 BIN R VALUE (WORKING SET) : 0.2178 REMARK 3 BIN FREE R VALUE : 0.2387 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 51 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.35720 REMARK 3 B22 (A**2) : 0.58810 REMARK 3 B33 (A**2) : 1.76920 REMARK 3 B12 (A**2) : -0.83180 REMARK 3 B13 (A**2) : -1.59110 REMARK 3 B23 (A**2) : 0.42440 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.390 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.155 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.139 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.231 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.141 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 318 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 564 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 62 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 4 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 44 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 318 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 4 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 18 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 382 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.69 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.15 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|333 - 343} REMARK 3 ORIGIN FOR THE GROUP (A): 1.5567 -1.5670 8.5522 REMARK 3 T TENSOR REMARK 3 T11: 0.0123 T22: -0.0584 REMARK 3 T33: -0.0025 T12: 0.0212 REMARK 3 T13: -0.0136 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 0.4446 L22: 0.7719 REMARK 3 L33: 0.1413 L12: 0.1553 REMARK 3 L13: 0.2583 L23: -0.0029 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: 0.0150 S13: -0.0193 REMARK 3 S21: 0.0345 S22: 0.0214 S23: 0.0100 REMARK 3 S31: -0.0012 S32: 0.0081 S33: -0.0036 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {B|333 - 343} REMARK 3 ORIGIN FOR THE GROUP (A): 0.0723 2.9365 8.5141 REMARK 3 T TENSOR REMARK 3 T11: -0.0034 T22: -0.0112 REMARK 3 T33: -0.0578 T12: 0.0524 REMARK 3 T13: 0.0033 T23: -0.0393 REMARK 3 L TENSOR REMARK 3 L11: 0.1750 L22: 1.0478 REMARK 3 L33: 0.2632 L12: -0.3835 REMARK 3 L13: -0.2677 L23: 0.2212 REMARK 3 S TENSOR REMARK 3 S11: -0.0069 S12: -0.0133 S13: 0.0326 REMARK 3 S21: -0.0048 S22: 0.0206 S23: -0.0360 REMARK 3 S31: 0.0040 S32: 0.0056 S33: -0.0137 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6CFH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232662. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : 18-AUG-15 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 7.50 REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1819 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 240 RESOLUTION RANGE LOW (A) : 13.170 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 240 DATA REDUNDANCY : 4.230 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.50 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.55 REMARK 240 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 240 DATA REDUNDANCY IN SHELL : 2.37 REMARK 240 R MERGE FOR SHELL (I) : 0.85500 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER 2.7.17 REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: EICOSAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 1.000000 0.000000 0.000000 2.63645 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -9.23088 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 -2.63645 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.23088 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 8.56000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 11.19645 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -9.23088 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 5.27291 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 -18.46176 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 -5.27291 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 18.46176 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 5.92355 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 9.23088 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 13.83291 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -18.46176 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 3.28709 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 18.46176 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN B 343 NE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6CB9 RELATED DB: PDB REMARK 900 RELATED ID: 6CEW RELATED DB: PDB REMARK 900 RELATED ID: 6CF4 RELATED DB: PDB REMARK 900 RELATED ID: EMD-7467 RELATED DB: EMDB REMARK 900 SWGMMGMLASQ SEGMENT FROM THE LOW COMPLEXITY DOMAIN OF TDP-43, REMARK 900 RESIDUES 333-343 DBREF 6CFH A 333 343 UNP Q13148 TADBP_HUMAN 333 343 DBREF 6CFH B 333 343 UNP Q13148 TADBP_HUMAN 333 343 SEQRES 1 A 11 SER TRP GLY MET MET GLY MET LEU ALA SER GLN SEQRES 1 B 11 SER TRP GLY MET MET GLY MET LEU ALA SER GLN SHEET 1 AA1 2 TRP A 334 SER A 342 0 SHEET 2 AA1 2 TRP B 334 SER B 342 -1 O SER B 342 N TRP A 334 CRYST1 8.560 9.600 39.970 97.17 92.89 105.94 P 1 2 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 0.116822 0.033366 0.010829 0.00000 SCALE2 0.000000 0.108332 0.015808 0.00000 SCALE3 0.000000 0.000000 0.025316 0.00000