HEADER PROTEIN FIBRIL 13-FEB-18 6CF4 TITLE SEGMENT NFGTFS, WITH FAMILIAL MUTATION A315T AND PHOSPHORYLATED TITLE 2 THREONINE, FROM THE LOW COMPLEXITY DOMAIN OF TDP-43, RESIDUES 312-317 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NFGTFS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 OTHER_DETAILS: SYNTHETIC PEPTIDE NFGPTFS CORRESPONDING TOSEGMENT SOURCE 6 312-317 OF TDP-43, WITH PHOSPHORYLATED THREONINE KEYWDS AMYLOID, LARKS, REVERSIBLE AGGREGATION, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR E.L.GUENTHER,Q.CAO,D.R.BOYER,M.R.SAWAYA,D.S.EISENBERG REVDAT 5 30-JUN-21 6CF4 1 REMARK REVDAT 4 18-DEC-19 6CF4 1 REMARK REVDAT 3 13-JUN-18 6CF4 1 JRNL REVDAT 2 06-JUN-18 6CF4 1 JRNL REVDAT 1 23-MAY-18 6CF4 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. 0.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 4178 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.240 REMARK 3 FREE R VALUE TEST SET COUNT : 428 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 7.6450 - 1.0815 0.85 1300 152 0.1861 0.2098 REMARK 3 2 1.0815 - 0.8588 0.88 1241 137 0.2828 0.2774 REMARK 3 3 0.8588 - 0.7503 0.88 1209 139 0.3819 0.4023 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.021 53 REMARK 3 ANGLE : 2.042 72 REMARK 3 CHIRALITY : 0.110 6 REMARK 3 PLANARITY : 0.008 9 REMARK 3 DIHEDRAL : 32.500 16 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6CF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232635. 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 : 09-JAN-18 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 : 4177 REMARK 240 RESOLUTION RANGE HIGH (A) : 0.750 REMARK 240 RESOLUTION RANGE LOW (A) : 7.645 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 240 DATA REDUNDANCY : 3.804 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :0.75 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :0.77 REMARK 240 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 240 DATA REDUNDANCY IN SHELL : 4.01 REMARK 240 R MERGE FOR SHELL (I) : 0.66100 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 11.82500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.03000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 15.03000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.82500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 2.36000 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 4.72000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 9.44000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 -4.72000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 -9.44000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 7.08000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 15.03000 REMARK 350 BIOMT1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 0.000000 1.000000 0.000000 2.36000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 15.03000 REMARK 350 BIOMT1 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 0.000000 1.000000 0.000000 -2.36000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 15.03000 REMARK 350 BIOMT1 9 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 -7.08000 REMARK 350 BIOMT3 9 0.000000 0.000000 -1.000000 15.03000 REMARK 350 BIOMT1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 10 0.000000 1.000000 0.000000 -11.80000 REMARK 350 BIOMT3 10 0.000000 0.000000 -1.000000 15.03000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O1P TPO A 315 HOP2 TPO A 315 1545 1.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WHN RELATED DB: PDB REMARK 900 RELATED ID: 5WKB RELATED DB: PDB REMARK 900 RELATED ID: 5WHP RELATED DB: PDB REMARK 900 RELATED ID: EMD-7466 RELATED DB: EMDB REMARK 900 SEGMENT NFGTFS, WITH FAMILIAL MUTATION A315T AND PHOSPHORYLATED REMARK 900 THREONINE, FROM THE LOW COMPLEXITY DOMAIN OF TDP-43, RESIDUES 312- REMARK 900 317 DBREF 6CF4 A 312 317 PDB 6CF4 6CF4 312 317 SEQRES 1 A 6 ASN PHE GLY TPO PHE SER HET TPO A 315 17 HETNAM TPO PHOSPHOTHREONINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 1 TPO C4 H10 N O6 P FORMUL 2 HOH *(H2 O) LINK C GLY A 314 N TPO A 315 1555 1555 1.32 LINK C TPO A 315 N PHE A 316 1555 1555 1.32 CRYST1 23.650 4.720 30.060 90.00 90.00 90.00 P 21 21 21 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 0.042283 0.000000 0.000000 0.00000 SCALE2 0.000000 0.211864 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033267 0.00000