HEADER MOTOR PROTEIN 16-AUG-22 8ARD TITLE MYOSIN VI PROXIMAL TAIL DOMAIN, DIMERIC COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCONVENTIONAL MYOSIN-VI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UNCONVENTIONAL MYOSIN-6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MYO6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DIMER, MYOSIN VI, MYO6, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.M.KIKUTI,H.SIRKIA,A.HOUDUSSE REVDAT 2 13-MAR-24 8ARD 1 JRNL REVDAT 1 30-AUG-23 8ARD 0 JRNL AUTH L.CANON,C.KIKUTI,V.J.PLANELLES-HERRERO,T.LIN,F.MAYEUX, JRNL AUTH 2 H.SIRKIA,Y.I.LEE,L.HEIDSIECK,L.VELIKOVSKY,A.DAVID,X.LIU, JRNL AUTH 3 D.MOUSSAOUI,E.FOREST,P.HOOK,K.J.PETERSEN,T.E.MORGAN, JRNL AUTH 4 A.DI CICCO,J.SIRES-CAMPOS,E.DERIVERY,D.LEVY,C.DELEVOYE, JRNL AUTH 5 H.L.SWEENEY,A.HOUDUSSE JRNL TITL HOW MYOSIN VI TRAPS ITS OFF-STATE, IS ACTIVATED AND JRNL TITL 2 DIMERIZES. JRNL REF NAT COMMUN V. 14 6732 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37872146 JRNL DOI 10.1038/S41467-023-42376-2 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.4 (8-JUN-2022) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 66.9 REMARK 3 NUMBER OF REFLECTIONS : 2977 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) : 0.324 REMARK 3 R VALUE (WORKING SET) : 0.323 REMARK 3 FREE R VALUE : 0.338 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 301 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.22 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.46 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 17.57 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3662 REMARK 3 BIN FREE R VALUE : 0.3562 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 23 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 512 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.65890 REMARK 3 B22 (A**2) : 3.65890 REMARK 3 B33 (A**2) : -7.31780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.630 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.899 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.384 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.895 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1046 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1904 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 348 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 159 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 512 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 69 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 891 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.60 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.58 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -8.4193 12.577 8.0757 REMARK 3 T TENSOR REMARK 3 T11: 0.3322 T22: -0.1552 REMARK 3 T33: -0.1929 T12: 0.0625 REMARK 3 T13: -0.1003 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 1.4077 L22: 0.4637 REMARK 3 L33: 16.6309 L12: 0.2596 REMARK 3 L13: 1.0147 L23: -5.23 REMARK 3 S TENSOR REMARK 3 S11: -0.2217 S12: 0.1845 S13: -0.9746 REMARK 3 S21: 0.1845 S22: -0.3542 S23: -0.2437 REMARK 3 S31: -0.9746 S32: -0.2437 S33: 0.576 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8ARD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124885. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978570 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20180409 REMARK 200 DATA SCALING SOFTWARE : STARANISO 1.10.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2977 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.219 REMARK 200 RESOLUTION RANGE LOW (A) : 49.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 66.9 REMARK 200 DATA REDUNDANCY : 18.20 REMARK 200 R MERGE (I) : 0.16800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.9 REMARK 200 DATA REDUNDANCY IN SHELL : 14.00 REMARK 200 R MERGE FOR SHELL (I) : 2.41400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 30X SER HELIX REMARK 200 REMARK 200 REMARK: THIN RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG 4000, 10 MM MGCL2, 0.2 M REMARK 280 IMIDAZOLE-MALATE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 197.09933 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 98.54967 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 147.82450 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 49.27483 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 246.37417 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 197.09933 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 98.54967 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 49.27483 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 147.82450 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 246.37417 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL 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 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 49.27483 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 872 REMARK 465 SER A 873 REMARK 465 MET A 874 REMARK 465 GLU A 875 REMARK 465 LYS A 938 REMARK 465 ARG A 939 REMARK 465 ARG A 940 DBREF 8ARD A 876 940 UNP E9Q3L1 E9Q3L1_MOUSE 876 940 SEQADV 8ARD GLY A 872 UNP E9Q3L1 EXPRESSION TAG SEQADV 8ARD SER A 873 UNP E9Q3L1 EXPRESSION TAG SEQADV 8ARD MET A 874 UNP E9Q3L1 EXPRESSION TAG SEQADV 8ARD GLU A 875 UNP E9Q3L1 EXPRESSION TAG SEQRES 1 A 69 GLY SER MET GLU ILE SER ILE ASP ALA LEU MET ALA LYS SEQRES 2 A 69 ILE LYS SER THR MET MET THR ARG GLU GLN ILE GLN LYS SEQRES 3 A 69 GLU TYR ASP ALA LEU VAL LYS SER SER GLU ASP LEU LEU SEQRES 4 A 69 SER ALA LEU GLN LYS LYS LYS GLN GLN GLU GLU GLU ALA SEQRES 5 A 69 GLU ARG LEU ARG ARG ILE GLN GLU GLU MET GLU LYS GLU SEQRES 6 A 69 ARG LYS ARG ARG FORMUL 2 HOH *5(H2 O) HELIX 1 AA1 ILE A 876 ARG A 937 1 62 CRYST1 29.387 29.387 295.649 90.00 90.00 120.00 P 65 2 2 12 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 0.034029 0.019646 0.000000 0.00000 SCALE2 0.000000 0.039293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003382 0.00000