HEADER ENDOCYTOSIS, PROTEIN BINDING 01-MAY-17 5VNY TITLE CRYSTAL STRUCTURE OF DM14-3 DOMAIN OF LGD COMPND MOL_ID: 1; COMPND 2 MOLECULE: LETHAL (2) GIANT DISCS 1, ISOFORM B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DM14-3 DOMAIN (UNP RESIDUES 359-423); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: L(2)GD1, CG4713, DMEL_CG4713; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ESCRT, ENDOCYTOSIS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.J.MCMILLAN,S.C.BLACKLOW REVDAT 1 14-JUN-17 5VNY 0 JRNL AUTH B.J.MCMILLAN,C.TIBBE,A.A.DRABEK,T.C.M.SEEGAR,S.C.BLACKLOW, JRNL AUTH 2 T.KLEIN JRNL TITL STRUCTURAL BASIS FOR REGULATION OF ESCRT-III COMPLEXES BY JRNL TITL 2 LGD. JRNL REF CELL REP V. 19 1750 2017 JRNL REFN ESSN 2211-1247 JRNL PMID 28564595 JRNL DOI 10.1016/J.CELREP.2017.05.026 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 46256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.680 REMARK 3 FREE R VALUE TEST SET COUNT : 3554 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 34.7949 - 3.2176 1.00 1763 146 0.1629 0.1694 REMARK 3 2 3.2176 - 2.5542 1.00 1798 142 0.1578 0.1785 REMARK 3 3 2.5542 - 2.2314 1.00 1765 151 0.1461 0.1549 REMARK 3 4 2.2314 - 2.0274 1.00 1791 151 0.1572 0.1681 REMARK 3 5 2.0274 - 1.8821 1.00 1745 142 0.1526 0.1476 REMARK 3 6 1.8821 - 1.7711 1.00 1781 148 0.1549 0.1833 REMARK 3 7 1.7711 - 1.6824 1.00 1792 148 0.1502 0.1692 REMARK 3 8 1.6824 - 1.6092 1.00 1773 149 0.1500 0.1577 REMARK 3 9 1.6092 - 1.5472 1.00 1757 143 0.1567 0.1724 REMARK 3 10 1.5472 - 1.4938 1.00 1795 150 0.1616 0.1832 REMARK 3 11 1.4938 - 1.4471 1.00 1770 145 0.1706 0.1620 REMARK 3 12 1.4471 - 1.4058 1.00 1752 156 0.1849 0.2026 REMARK 3 13 1.4058 - 1.3688 1.00 1816 153 0.1913 0.1879 REMARK 3 14 1.3688 - 1.3354 1.00 1766 145 0.1931 0.1964 REMARK 3 15 1.3354 - 1.3050 1.00 1746 147 0.1937 0.2044 REMARK 3 16 1.3050 - 1.2772 1.00 1775 148 0.1976 0.1961 REMARK 3 17 1.2772 - 1.2517 1.00 1763 149 0.2079 0.1933 REMARK 3 18 1.2517 - 1.2281 1.00 1773 145 0.2078 0.1956 REMARK 3 19 1.2281 - 1.2061 1.00 1786 150 0.2222 0.2157 REMARK 3 20 1.2061 - 1.1857 0.99 1723 148 0.2312 0.2332 REMARK 3 21 1.1857 - 1.1666 0.99 1797 146 0.2445 0.2217 REMARK 3 22 1.1666 - 1.1486 0.94 1663 142 0.2599 0.2403 REMARK 3 23 1.1486 - 1.1317 0.89 1587 125 0.2663 0.2773 REMARK 3 24 1.1317 - 1.1158 0.70 1253 106 0.3146 0.2866 REMARK 3 25 1.1158 - 1.1007 0.56 972 79 0.3307 0.3373 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 524 REMARK 3 ANGLE : 0.897 705 REMARK 3 CHIRALITY : 0.067 72 REMARK 3 PLANARITY : 0.008 95 REMARK 3 DIHEDRAL : 17.431 208 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 18.2458 26.5643 60.2038 REMARK 3 T TENSOR REMARK 3 T11: 0.0991 T22: 0.1454 REMARK 3 T33: 0.1149 T12: 0.0003 REMARK 3 T13: 0.0021 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 0.0289 L22: 0.0669 REMARK 3 L33: 0.1477 L12: 0.0119 REMARK 3 L13: 0.0588 L23: -0.0353 REMARK 3 S TENSOR REMARK 3 S11: -0.0126 S12: 0.0798 S13: 0.0280 REMARK 3 S21: 0.0034 S22: -0.0018 S23: 0.0516 REMARK 3 S31: -0.0413 S32: -0.0448 S33: 0.0079 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 5VNY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227742. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYO-COOLED DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 11.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.96200 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG2000 MME, TRIS, PH 8.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 69.55500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 14.83500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 14.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.77750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 14.83500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 14.83500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 104.33250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 14.83500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 14.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.77750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 14.83500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 14.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 104.33250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.55500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 578 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 589 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 612 LIES ON A SPECIAL POSITION. 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 SER A 358 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 618 DISTANCE = 6.31 ANGSTROMS DBREF 5VNY A 359 423 UNP M9NEZ0 M9NEZ0_DROME 359 423 SEQADV 5VNY SER A 358 UNP M9NEZ0 EXPRESSION TAG SEQRES 1 A 66 SER THR ASN MSE LEU GLU ALA LEU GLN GLN ARG LEU GLU SEQRES 2 A 66 LYS TYR GLN SER VAL GLU ALA ALA ALA LYS ALA GLU ASN SEQRES 3 A 66 ASN SER GLY LYS ALA ARG ARG PHE GLY ARG ILE VAL LYS SEQRES 4 A 66 GLN TYR GLU ASP ALA ILE LYS LEU TYR LYS ALA GLY LYS SEQRES 5 A 66 PRO VAL PRO TYR ASP GLU LEU PRO VAL PRO PRO GLY PHE SEQRES 6 A 66 GLY MODRES 5VNY MSE A 361 MET MODIFIED RESIDUE HET MSE A 361 17 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *118(H2 O) HELIX 1 AA1 ASN A 360 ALA A 381 1 22 HELIX 2 AA2 ASN A 384 ALA A 407 1 24 HELIX 3 AA3 PRO A 412 LEU A 416 5 5 LINK C ASN A 360 N MSE A 361 1555 1555 1.33 LINK C MSE A 361 N LEU A 362 1555 1555 1.34 CRYST1 29.670 29.670 139.110 90.00 90.00 90.00 P 41 21 2 8 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 0.033704 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007189 0.00000