HEADER PROTEIN FIBRIL 24-SEP-21 7VI5 TITLE ELECTRON CRYSTALLOGRAPHIC STRUCTURE OF TIA-1 PRION-LIKE DOMAIN, WILD TITLE 2 TYPE SEQUENCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TIA-1 PRION-LIKE DOMAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA-BINDING PROTEIN TIA-1,T-CELL-RESTRICTED INTRACELLULAR COMPND 5 ANTIGEN-1,TIA-1,P40-TIA-1; 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 ALS, PRION, FIBRIL, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR K.TAKABA,S.MAKI-YONEKURA,N.SEKIYAMA,K.IMAMURA,T.KODAMA,H.TOCHIO, AUTHOR 2 K.YONEKURA REVDAT 2 29-NOV-23 7VI5 1 REMARK REVDAT 1 28-SEP-22 7VI5 0 JRNL AUTH N.SEKIYAMA,K.TAKABA,S.MAKI-YONEKURA,K.I.AKAGI,Y.OHTANI, JRNL AUTH 2 K.IMAMURA,T.TERAKAWA,K.YAMASHITA,D.INAOKA,K.YONEKURA, JRNL AUTH 3 T.S.KODAMA,H.TOCHIO JRNL TITL ALS MUTATIONS IN THE TIA-1 PRION-LIKE DOMAIN TRIGGER HIGHLY JRNL TITL 2 CONDENSED PATHOGENIC STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 23119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 36112647 JRNL DOI 10.1073/PNAS.2122523119 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 1149 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.284 REMARK 3 R VALUE (WORKING SET) : 0.277 REMARK 3 FREE R VALUE : 0.347 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 114 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 18.8660 - 3.7838 0.99 117 15 0.2845 0.2532 REMARK 3 2 3.7838 - 3.0072 1.00 106 11 0.2888 0.3303 REMARK 3 3 3.0072 - 2.6282 1.00 104 10 0.2997 0.3853 REMARK 3 4 2.6282 - 2.3884 1.00 100 9 0.2879 0.4613 REMARK 3 5 2.3884 - 2.2175 1.00 111 14 0.2875 0.3265 REMARK 3 6 2.2175 - 2.0870 1.00 97 9 0.3267 0.3692 REMARK 3 7 2.0870 - 1.9826 1.00 94 12 0.2727 0.2723 REMARK 3 8 1.9826 - 1.8964 1.00 98 11 0.2855 0.3799 REMARK 3 9 1.8964 - 1.8234 1.00 111 11 0.2337 0.5376 REMARK 3 10 1.8234 - 1.7610 1.00 97 12 0.2168 0.2729 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.14 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 : 0.009 77 REMARK 3 ANGLE : 1.072 103 REMARK 3 CHIRALITY : 0.080 10 REMARK 3 PLANARITY : 0.005 13 REMARK 3 DIHEDRAL : 9.935 25 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 7VI5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024728. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : FILAMENT REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : JEOL CRYO ARM 300 REMARK 240 DETECTOR TYPE : DIRECT ELECTRON DE-64 (8K X 8K) REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : 7VI4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 6.42000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 3.21000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 4.81500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 1.60500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 8.02500 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: MONOMERIC 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 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 A 10 CG CD OE1 NE2 DBREF 7VI5 A 1 10 UNP P31483 TIA1_HUMAN 377 386 SEQRES 1 A 10 GLY TYR ARG VAL ALA GLY TYR GLU THR GLN CRYST1 43.570 43.570 9.630 90.00 90.00 120.00 P 65 6 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 0.022952 0.013251 0.000000 0.00000 SCALE2 0.000000 0.026502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.103842 0.00000 ATOM 1 N GLY A 1 19.379 33.391 -0.960 1.00 3.57 N ATOM 2 CA GLY A 1 18.513 32.353 -1.511 1.00 16.06 C ATOM 3 C GLY A 1 18.103 31.280 -0.517 1.00 6.28 C ATOM 4 O GLY A 1 18.375 31.379 0.688 1.00 5.94 O ATOM 5 N TYR A 2 17.448 30.226 -1.008 1.00 3.68 N ATOM 6 CA TYR A 2 16.939 29.164 -0.140 1.00 15.22 C ATOM 7 C TYR A 2 16.703 27.923 -0.983 1.00 5.61 C ATOM 8 O TYR A 2 16.715 27.971 -2.214 1.00 11.76 O ATOM 9 CB TYR A 2 15.628 29.560 0.554 1.00 6.40 C ATOM 10 CG TYR A 2 14.498 29.660 -0.442 1.00 9.68 C ATOM 11 CD1 TYR A 2 13.651 28.587 -0.662 1.00 12.41 C ATOM 12 CD2 TYR A 2 14.292 30.816 -1.183 1.00 13.24 C ATOM 13 CE1 TYR A 2 12.630 28.652 -1.573 1.00 15.05 C ATOM 14 CE2 TYR A 2 13.264 30.895 -2.116 1.00 18.51 C ATOM 15 CZ TYR A 2 12.431 29.806 -2.302 1.00 13.94 C ATOM 16 OH TYR A 2 11.401 29.855 -3.204 1.00 21.28 O ATOM 17 N ARG A 3 16.484 26.808 -0.296 1.00 2.49 N ATOM 18 CA ARG A 3 16.184 25.536 -0.930 1.00 7.30 C ATOM 19 C ARG A 3 15.086 24.843 -0.142 1.00 10.10 C ATOM 20 O ARG A 3 14.959 25.067 1.067 1.00 0.01 O ATOM 21 CB ARG A 3 17.439 24.649 -1.008 1.00 27.37 C ATOM 22 CG ARG A 3 18.090 24.348 0.341 1.00 9.88 C ATOM 23 CD ARG A 3 19.485 23.776 0.078 1.00 18.49 C ATOM 24 NE ARG A 3 20.184 23.227 1.233 1.00 24.97 N ATOM 25 CZ ARG A 3 20.872 23.939 2.121 1.00 33.34 C ATOM 26 NH1 ARG A 3 20.959 25.252 2.009 1.00 18.30 N ATOM 27 NH2 ARG A 3 21.480 23.326 3.129 1.00 27.58 N ATOM 28 N VAL A 4 14.337 23.969 -0.827 1.00 8.53 N ATOM 29 CA VAL A 4 13.126 23.345 -0.288 1.00 5.22 C ATOM 30 C VAL A 4 12.799 22.100 -1.114 1.00 6.70 C ATOM 31 O VAL A 4 13.076 22.041 -2.318 1.00 7.66 O ATOM 32 CB VAL A 4 11.942 24.360 -0.245 1.00 0.45 C ATOM 33 CG1 VAL A 4 11.577 24.901 -1.601 1.00 4.90 C ATOM 34 CG2 VAL A 4 10.738 23.774 0.538 1.00 9.39 C ATOM 35 N ALA A 5 12.187 21.108 -0.466 1.00 8.94 N ATOM 36 CA ALA A 5 11.919 19.824 -1.116 1.00 3.32 C ATOM 37 C ALA A 5 10.873 19.076 -0.296 1.00 5.49 C ATOM 38 O ALA A 5 10.671 19.351 0.896 1.00 3.57 O ATOM 39 CB ALA A 5 13.212 19.018 -1.286 1.00 3.32 C ATOM 40 N GLY A 6 10.187 18.157 -0.959 1.00 3.42 N ATOM 41 CA GLY A 6 9.097 17.411 -0.343 1.00 9.04 C ATOM 42 C GLY A 6 8.944 16.056 -0.996 1.00 11.52 C ATOM 43 O GLY A 6 9.286 15.871 -2.168 1.00 12.84 O ATOM 44 N TYR A 7 8.403 15.103 -0.239 1.00 6.08 N ATOM 45 CA TYR A 7 8.168 13.752 -0.752 1.00 5.60 C ATOM 46 C TYR A 7 7.021 13.139 0.032 1.00 12.40 C ATOM 47 O TYR A 7 6.880 13.355 1.246 1.00 3.09 O ATOM 48 CB TYR A 7 9.431 12.854 -0.663 1.00 6.92 C ATOM 49 CG TYR A 7 9.253 11.389 -1.057 1.00 9.18 C ATOM 50 CD1 TYR A 7 9.775 10.884 -2.250 1.00 7.61 C ATOM 51 CD2 TYR A 7 8.569 10.502 -0.224 1.00 19.78 C ATOM 52 CE1 TYR A 7 9.591 9.545 -2.595 1.00 9.76 C ATOM 53 CE2 TYR A 7 8.387 9.184 -0.554 1.00 15.17 C ATOM 54 CZ TYR A 7 8.888 8.695 -1.723 1.00 3.39 C ATOM 55 OH TYR A 7 8.679 7.363 -2.015 1.00 8.22 O ATOM 56 N GLU A 8 6.224 12.342 -0.676 1.00 5.25 N ATOM 57 CA GLU A 8 5.042 11.717 -0.111 1.00 10.43 C ATOM 58 C GLU A 8 4.698 10.489 -0.935 1.00 17.41 C ATOM 59 O GLU A 8 4.747 10.529 -2.171 1.00 6.33 O ATOM 60 CB GLU A 8 3.867 12.697 -0.104 1.00 11.03 C ATOM 61 CG GLU A 8 2.678 12.291 0.712 1.00 24.83 C ATOM 62 CD GLU A 8 1.659 13.406 0.774 1.00 25.57 C ATOM 63 OE1 GLU A 8 2.071 14.579 0.793 1.00 25.01 O ATOM 64 OE2 GLU A 8 0.451 13.118 0.742 1.00 17.96 O ATOM 65 N THR A 9 4.343 9.405 -0.242 1.00 13.21 N ATOM 66 CA THR A 9 3.770 8.245 -0.912 1.00 23.57 C ATOM 67 C THR A 9 2.436 8.624 -1.553 1.00 15.62 C ATOM 68 O THR A 9 1.697 9.459 -1.033 1.00 15.23 O ATOM 69 CB THR A 9 3.605 7.093 0.089 1.00 18.24 C ATOM 70 OG1 THR A 9 4.899 6.659 0.522 1.00 10.95 O ATOM 71 CG2 THR A 9 2.871 5.889 -0.534 1.00 19.54 C ATOM 72 N GLN A 10 2.161 8.044 -2.721 1.00 19.48 N ATOM 73 CA GLN A 10 0.915 8.264 -3.471 1.00 12.49 C ATOM 74 C GLN A 10 0.801 9.705 -3.923 1.00 21.03 C ATOM 75 O GLN A 10 1.432 10.106 -4.906 1.00 24.92 O ATOM 76 CB GLN A 10 -0.310 7.864 -2.642 1.00 14.34 C TER 77 GLN A 10 MASTER 183 0 0 0 0 0 0 6 76 1 0 1 END