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