HEADER PROTEIN FIBRIL 13-JUN-17 5W52 TITLE MICROED STRUCTURE OF THE SEGMENT, DLIIKGISVHI, FROM THE RRM2 OF TDP- TITLE 2 43, RESIDUES 247-257 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR DNA-BINDING PROTEIN 43; COMPND 3 CHAIN: A; 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 CRYSTALLOGRAPHY AUTHOR E.L.GUENTHER,M.R.SAWAYA,D.CASCIO,D.S.EISENBERG REVDAT 10 03-APR-24 5W52 1 REMARK REVDAT 9 13-MAR-24 5W52 1 REMARK REVDAT 8 30-JUN-21 5W52 1 REMARK REVDAT 7 27-NOV-19 5W52 1 REMARK REVDAT 6 06-JUN-18 5W52 1 REMARK REVDAT 5 25-APR-18 5W52 1 REMARK REVDAT 4 18-APR-18 5W52 1 JRNL REVDAT 3 28-MAR-18 5W52 1 JRNL REVDAT 2 14-MAR-18 5W52 1 JRNL REVDAT 1 21-FEB-18 5W52 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. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 72.0 REMARK 3 NUMBER OF REFLECTIONS : 944 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) : 0.266 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.900 REMARK 3 FREE R VALUE TEST SET COUNT : 92 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 84 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) : 21.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 20.78000 REMARK 3 B22 (A**2) : -25.77000 REMARK 3 B33 (A**2) : 4.98000 REMARK 3 B12 (A**2) : -1.04000 REMARK 3 B13 (A**2) : -18.05000 REMARK 3 B23 (A**2) : -3.48000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.788 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 5W52 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_1000228456. 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 : 19-JAN-17 REMARK 240 TEMPERATURE (KELVIN) : 100.0 REMARK 240 PH : 8.50 REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TECNAI 20 REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 1037 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 240 RESOLUTION RANGE LOW (A) : 15.600 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 73.4 REMARK 240 DATA REDUNDANCY : 9.019 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.40 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.48 REMARK 240 COMPLETENESS FOR SHELL (%) : 62.1 REMARK 240 DATA REDUNDANCY IN SHELL : 6.71 REMARK 240 R MERGE FOR SHELL (I) : 1.45100 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : IDEALIZED 11-RESIDUE BETA REMARK 240 STRAND 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: 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 0.01816 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.72997 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 0.03632 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.45993 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 -0.01816 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -4.72997 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 -0.03632 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -9.45993 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 -1.00225 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 -2.50527 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 -15.59833 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 7 1.000000 0.000000 0.000000 -0.98408 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 2.22470 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 -15.59833 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 8 1.000000 0.000000 0.000000 -0.96592 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 6.95466 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 -15.59833 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 -1.02041 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -7.23523 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 -15.59833 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 10 1.000000 0.000000 0.000000 -1.03857 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 -11.96520 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -15.59833 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5W50 RELATED DB: PDB REMARK 900 RELATED ID: EMD-8765 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF THE SEGMENT, DLIIKGISVHI, FROM THE RRM2 OF TDP- REMARK 900 43, RESIDUES 247-257 DBREF 5W52 A 1 11 UNP Q13148 TADBP_HUMAN 247 257 SEQRES 1 A 11 ASP LEU ILE ILE LYS GLY ILE SER VAL HIS ILE CRYST1 24.810 4.730 15.830 80.88 86.37 89.78 P 1 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 0.040306 -0.000158 -0.002562 0.00000 SCALE2 0.000000 0.211418 -0.033974 0.00000 SCALE3 0.000000 0.000000 0.064110 0.00000