HEADER PROTEIN TRANSPORT 01-NOV-24 9E7C TITLE TRK-FUSED GENE (TFG) PB1 DOMAIN D60A/D62R VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN TFG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRK-FUSED GENE PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: THE FIRST 9 N-TERMINAL AMINO ACIDS OF TFG AS WELL AS COMPND 8 THE GST PROTEIN PURIFICATION TAG WERE NOT WELL RESOLVED IN THE COMPND 9 DIFFRACTION DATA AND THEREFORE NOT INCLUDED IN THE FINAL STRUCTURE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TFG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS TYPE I/II PB1 DOMAIN, OCTAMER, UBIQUITIN LIKE BETA-GRASP FOLD, KEYWDS 2 GLOBULAR, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.L.SCHUH,B.BHATTACHARYYA,J.L.KECK,A.AUDHYA REVDAT 1 20-NOV-24 9E7C 0 JRNL AUTH Z.ZHANG,M.M.LETTMAN,A.L.SCHUH,B.BHATTACHARYYA,P.RANDOLPH, JRNL AUTH 2 T.NANDAKUMAR,I.KULKARNI,A.ROACH,J.R.ALVIN,D.GENGLER, JRNL AUTH 3 S.M.STAGG,J.L.KECK,A.AUDHYA JRNL TITL MULTIPLE ROLES FOR TFG RING COMPLEXES IN NEURONAL CARGO JRNL TITL 2 TRAFFICKING JRNL REF BIORXIV 2024 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2024.11.05.621662 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 7337 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 352 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 492 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 19 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.83000 REMARK 3 B22 (A**2) : 2.64000 REMARK 3 B33 (A**2) : -0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.67000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.175 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.496 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 723 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 735 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 974 ; 1.342 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1690 ; 0.749 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 88 ; 5.918 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 33 ;37.044 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 145 ;12.902 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;12.960 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 114 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 798 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 159 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 352 ; 2.876 ; 3.144 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 351 ; 2.866 ; 3.136 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 440 ; 5.019 ; 4.687 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 441 ; 5.018 ; 4.695 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 371 ; 2.896 ; 3.700 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 371 ; 2.889 ; 3.698 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 534 ; 5.039 ; 5.355 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 796 ; 8.606 ;25.074 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 777 ; 8.505 ;24.878 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9E7C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1000289453. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 203 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.906 REMARK 200 RESOLUTION RANGE LOW (A) : 51.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53600 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.5, 8% PEG 8000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 53.50900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.24400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.50900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.24400 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 ASP A 6 REMARK 465 LEU A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 DBREF 9E7C A 1 96 UNP Q92734 TFG_HUMAN 1 96 SEQADV 9E7C GLY A -4 UNP Q92734 EXPRESSION TAG SEQADV 9E7C PRO A -3 UNP Q92734 EXPRESSION TAG SEQADV 9E7C LEU A -2 UNP Q92734 EXPRESSION TAG SEQADV 9E7C GLY A -1 UNP Q92734 EXPRESSION TAG SEQADV 9E7C SER A 0 UNP Q92734 EXPRESSION TAG SEQADV 9E7C ALA A 60 UNP Q92734 ASP 60 ENGINEERED MUTATION SEQADV 9E7C ARG A 62 UNP Q92734 ASP 62 ENGINEERED MUTATION SEQRES 1 A 101 GLY PRO LEU GLY SER MET ASN GLY GLN LEU ASP LEU SER SEQRES 2 A 101 GLY LYS LEU ILE ILE LYS ALA GLN LEU GLY GLU ASP ILE SEQRES 3 A 101 ARG ARG ILE PRO ILE HIS ASN GLU ASP ILE THR TYR ASP SEQRES 4 A 101 GLU LEU VAL LEU MET MET GLN ARG VAL PHE ARG GLY LYS SEQRES 5 A 101 LEU LEU SER ASN ASP GLU VAL THR ILE LYS TYR LYS ALA SEQRES 6 A 101 GLU ARG GLY ASP LEU ILE THR ILE PHE ASP SER SER ASP SEQRES 7 A 101 LEU SER PHE ALA ILE GLN CYS SER ARG ILE LEU LYS LEU SEQRES 8 A 101 THR LEU PHE VAL ASN GLY GLN PRO ARG PRO FORMUL 2 HOH *51(H2 O) HELIX 1 AA1 THR A 32 PHE A 44 1 13 HELIX 2 AA2 ARG A 45 LEU A 48 5 4 HELIX 3 AA3 ASP A 70 CYS A 80 1 11 SHEET 1 AA1 2 LEU A 11 LEU A 17 0 SHEET 2 AA1 2 ASP A 20 ILE A 26 -1 O ILE A 24 N ILE A 13 SHEET 1 AA2 2 ILE A 56 LYS A 59 0 SHEET 2 AA2 2 LEU A 65 ILE A 68 -1 O ILE A 68 N ILE A 56 CRYST1 107.018 32.488 29.246 90.00 104.80 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 0.009344 0.000000 0.002468 0.00000 SCALE2 0.000000 0.030781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035365 0.00000