HEADER PROTEIN FIBRIL 25-JUL-17 5WKD TITLE CRYSTAL STRUCTURE OF THE SEGMENT, GNNQGSN, FROM THE LOW COMPLEXITY TITLE 2 DOMAIN OF TDP-43, RESIDUES 300-306 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR DNA-BINDING PROTEIN 43; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 300-306; 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 KEYWDS TDP-43, AMYLOID, LOW COMPLEXITY DOMAIN, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR E.L.GUENTHER,H.TRINH,M.R.SAWAYA,D.CASCIO,D.S.EISENBERG REVDAT 8 03-APR-24 5WKD 1 REMARK REVDAT 7 13-MAR-24 5WKD 1 REMARK REVDAT 6 18-DEC-19 5WKD 1 REMARK REVDAT 5 20-FEB-19 5WKD 1 REMARK REVDAT 4 20-JUN-18 5WKD 1 JRNL REVDAT 3 06-JUN-18 5WKD 1 JRNL REVDAT 2 30-MAY-18 5WKD 1 JRNL REVDAT 1 18-APR-18 5WKD 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. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 345 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 22 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 48 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : 0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5WKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000229073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 373 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.15800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: IDEALIZED BETA STRAND REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 2.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PROPANE, PH 7.5, 200 MM REMARK 280 SODIUM SULFATE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 25.17350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.38850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.17350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.38850 REMARK 290 SMTRY3 4 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.77700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.55400 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -4.77700 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -9.55400 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 25.17350 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 2.38850 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 25.17350 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 7.16550 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 25.17350 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 11.94250 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 25.17350 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -2.38850 REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 25.17350 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 -7.16550 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 401 LIES ON A SPECIAL POSITION. DBREF 5WKD A 300 306 UNP Q13148 TADBP_HUMAN 300 306 SEQRES 1 A 7 GLY ASN ASN GLN GLY SER ASN FORMUL 2 HOH *2(H2 O) CRYST1 50.347 4.777 14.746 90.00 101.73 90.00 C 1 2 1 4 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 0.019862 0.000000 0.004125 0.00000 SCALE2 0.000000 0.209336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.069262 0.00000 ATOM 1 N GLY A 300 0.958 0.885 3.506 1.00 13.41 N ATOM 2 CA GLY A 300 2.189 0.130 3.261 1.00 11.45 C ATOM 3 C GLY A 300 3.414 0.816 3.766 1.00 10.36 C ATOM 4 O GLY A 300 3.427 2.050 3.946 1.00 9.06 O ATOM 5 N ASN A 301 4.441 -0.005 3.969 1.00 8.48 N ATOM 6 CA ASN A 301 5.752 0.443 4.412 1.00 10.23 C ATOM 7 C ASN A 301 6.828 -0.143 3.505 1.00 8.85 C ATOM 8 O ASN A 301 6.776 -1.337 3.163 1.00 7.98 O ATOM 9 CB ASN A 301 6.006 -0.049 5.828 1.00 11.40 C ATOM 10 CG ASN A 301 5.126 0.629 6.880 1.00 16.85 C ATOM 11 OD1 ASN A 301 4.735 -0.040 7.857 1.00 24.53 O ATOM 12 ND2 ASN A 301 4.822 1.937 6.717 1.00 15.59 N ATOM 13 N ASN A 302 7.781 0.706 3.092 1.00 7.99 N ATOM 14 CA ASN A 302 8.977 0.318 2.342 1.00 6.37 C ATOM 15 C ASN A 302 10.144 0.930 3.095 1.00 5.74 C ATOM 16 O ASN A 302 10.139 2.121 3.335 1.00 4.44 O ATOM 17 CB ASN A 302 8.907 0.767 0.863 1.00 7.61 C ATOM 18 CG ASN A 302 7.687 0.222 0.186 1.00 6.18 C ATOM 19 OD1 ASN A 302 7.544 -0.988 0.138 1.00 6.49 O ATOM 20 ND2 ASN A 302 6.752 1.071 -0.209 1.00 6.54 N ATOM 21 N GLN A 303 11.123 0.091 3.421 1.00 5.85 N ATOM 22 CA GLN A 303 12.339 0.491 4.084 1.00 6.53 C ATOM 23 C GLN A 303 13.553 -0.176 3.442 1.00 7.08 C ATOM 24 O GLN A 303 13.543 -1.391 3.298 1.00 7.14 O ATOM 25 CB GLN A 303 12.238 0.037 5.494 1.00 7.41 C ATOM 26 CG GLN A 303 13.445 0.409 6.333 1.00 9.08 C ATOM 27 CD GLN A 303 13.208 0.022 7.714 1.00 9.34 C ATOM 28 OE1 GLN A 303 13.186 -1.168 8.041 1.00 11.92 O ATOM 29 NE2 GLN A 303 12.938 0.994 8.522 1.00 8.56 N ATOM 30 N GLY A 304 14.611 0.578 3.107 1.00 6.92 N ATOM 31 CA GLY A 304 15.837 -0.029 2.607 1.00 7.01 C ATOM 32 C GLY A 304 17.086 0.682 3.069 1.00 8.20 C ATOM 33 O GLY A 304 17.093 1.900 3.287 1.00 9.03 O ATOM 34 N SER A 305 18.183 -0.053 3.159 1.00 8.14 N ATOM 35 CA SER A 305 19.433 0.516 3.537 1.00 7.93 C ATOM 36 C SER A 305 20.546 -0.109 2.760 1.00 7.64 C ATOM 37 O SER A 305 20.581 -1.341 2.608 1.00 5.66 O ATOM 38 CB SER A 305 19.664 0.285 5.045 1.00 10.87 C ATOM 39 OG SER A 305 19.910 -1.065 5.271 1.00 12.12 O ATOM 40 N ASN A 306 21.497 0.739 2.326 1.00 7.94 N ATOM 41 CA ASN A 306 22.687 0.282 1.614 1.00 9.04 C ATOM 42 C ASN A 306 23.906 0.883 2.357 1.00 15.55 C ATOM 43 O ASN A 306 23.769 1.630 3.382 1.00 18.57 O ATOM 44 CB ASN A 306 22.679 0.726 0.136 1.00 9.12 C ATOM 45 CG ASN A 306 21.520 0.146 -0.601 1.00 10.74 C ATOM 46 OD1 ASN A 306 21.411 -1.102 -0.709 1.00 15.42 O ATOM 47 ND2 ASN A 306 20.643 1.001 -1.125 1.00 10.39 N ATOM 48 OXT ASN A 306 25.061 0.620 1.925 1.00 21.94 O TER 49 ASN A 306 HETATM 50 O HOH A 401 25.165 2.934 0.008 0.50 23.31 O HETATM 51 O HOH A 402 12.554 -2.226 0.065 1.00 13.65 O MASTER 234 0 0 0 0 0 0 6 50 1 0 1 END