HEADER STRUCTURAL PROTEIN/TRANSPORT PROTEIN 17-FEB-12 4DS1 TITLE THE STRUCTURE OF A YEAST DYN2-NUP159 COMPLEX AND THE MOLECULAR BASIS TITLE 2 FOR THE DYNEIN LIGHT CHAIN - NUCLEAR PORE INTERACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NUCLEOPORIN NUP159; COMPND 7 CHAIN: B, D; COMPND 8 FRAGMENT: UNP RESIDUES 1116-1126; COMPND 9 SYNONYM: NUCLEAR PORE PROTEIN NUP159; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 GENE: DYN2, SLC1, YDR424C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-6P2; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 15 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 16 ORGANISM_TAXID: 559292 KEYWDS NUCLEOPORIN, DYNEIN LIGHT CHAIN FOLD, PEPTIDE BINDING, NUCLEAR PORE, KEYWDS 2 STRUCTURAL PROTEIN-TRANSPORT PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.C.SLEP,E.M.ROMES REVDAT 4 13-SEP-23 4DS1 1 SEQADV REVDAT 3 25-JUL-12 4DS1 1 JRNL REVDAT 2 18-APR-12 4DS1 1 JRNL REVDAT 1 21-MAR-12 4DS1 0 JRNL AUTH E.M.ROMES,A.TRIPATHY,K.C.SLEP JRNL TITL STRUCTURE OF A YEAST DYN2-NUP159 COMPLEX AND MOLECULAR BASIS JRNL TITL 2 FOR DYNEIN LIGHT CHAIN-NUCLEAR PORE INTERACTION. JRNL REF J.BIOL.CHEM. V. 287 15862 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22411995 JRNL DOI 10.1074/JBC.M111.336172 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 14920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1490 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 29.2522 - 3.9838 1.00 1560 174 0.1497 0.1834 REMARK 3 2 3.9838 - 3.1633 1.00 1471 163 0.1485 0.1589 REMARK 3 3 3.1633 - 2.7638 1.00 1447 160 0.1589 0.1858 REMARK 3 4 2.7638 - 2.5112 1.00 1428 158 0.1638 0.2193 REMARK 3 5 2.5112 - 2.3313 1.00 1437 159 0.1510 0.2070 REMARK 3 6 2.3313 - 2.1939 0.99 1407 154 0.1437 0.1963 REMARK 3 7 2.1939 - 2.0841 0.99 1408 157 0.1411 0.1824 REMARK 3 8 2.0841 - 1.9934 0.93 1316 148 0.1450 0.1779 REMARK 3 9 1.9934 - 1.9166 0.78 1109 123 0.1440 0.1893 REMARK 3 10 1.9166 - 1.8505 0.60 847 94 0.1801 0.2472 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 36.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64100 REMARK 3 B22 (A**2) : 3.47080 REMARK 3 B33 (A**2) : -2.82980 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 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 1573 REMARK 3 ANGLE : 1.020 2127 REMARK 3 CHIRALITY : 0.071 243 REMARK 3 PLANARITY : 0.003 263 REMARK 3 DIHEDRAL : 12.475 563 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 4DS1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000070709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : COPPER KALPHA / OSMIC MIRRORS REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15081 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 29.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15000 REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2PG1 LACKING BOUND PEPTIDE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M AMMONIUM ACETATE, 5% METHYL REMARK 280 PENTANEDIOL (V/V), 35% PEG 4000 (W/V), PH 5.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.93450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.35150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.98550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.35150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.93450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.98550 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 ASN B 1116 REMARK 465 GLY C -4 REMARK 465 PRO C -3 REMARK 465 LEU C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 ASP C 3 REMARK 465 GLU C 4 REMARK 465 ASN C 5 REMARK 465 LYS C 6 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 ASN D1116 CG OD1 ND2 DBREF 4DS1 A 1 92 UNP Q02647 DYL1_YEAST 1 92 DBREF 4DS1 B 1116 1126 UNP P40477 NU159_YEAST 1116 1126 DBREF 4DS1 C 1 92 UNP Q02647 DYL1_YEAST 1 92 DBREF 4DS1 D 1116 1126 UNP P40477 NU159_YEAST 1116 1126 SEQADV 4DS1 GLY A -4 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 PRO A -3 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 LEU A -2 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 GLY A -1 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 SER A 0 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 GLY C -4 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 PRO C -3 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 LEU C -2 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 GLY C -1 UNP Q02647 EXPRESSION TAG SEQADV 4DS1 SER C 0 UNP Q02647 EXPRESSION TAG SEQRES 1 A 97 GLY PRO LEU GLY SER MET SER ASP GLU ASN LYS SER THR SEQRES 2 A 97 PRO ILE VAL LYS ALA SER ASP ILE THR ASP LYS LEU LYS SEQRES 3 A 97 GLU ASP ILE LEU THR ILE SER LYS ASP ALA LEU ASP LYS SEQRES 4 A 97 TYR GLN LEU GLU ARG ASP ILE ALA GLY THR VAL LYS LYS SEQRES 5 A 97 GLN LEU ASP VAL LYS TYR GLY ASN THR TRP HIS VAL ILE SEQRES 6 A 97 VAL GLY LYS ASN PHE GLY SER TYR VAL THR HIS GLU LYS SEQRES 7 A 97 GLY HIS PHE VAL TYR PHE TYR ILE GLY PRO LEU ALA PHE SEQRES 8 A 97 LEU VAL PHE LYS THR ALA SEQRES 1 B 11 ASN TYR ALA GLU SER GLY ILE GLN THR ASP LEU SEQRES 1 C 97 GLY PRO LEU GLY SER MET SER ASP GLU ASN LYS SER THR SEQRES 2 C 97 PRO ILE VAL LYS ALA SER ASP ILE THR ASP LYS LEU LYS SEQRES 3 C 97 GLU ASP ILE LEU THR ILE SER LYS ASP ALA LEU ASP LYS SEQRES 4 C 97 TYR GLN LEU GLU ARG ASP ILE ALA GLY THR VAL LYS LYS SEQRES 5 C 97 GLN LEU ASP VAL LYS TYR GLY ASN THR TRP HIS VAL ILE SEQRES 6 C 97 VAL GLY LYS ASN PHE GLY SER TYR VAL THR HIS GLU LYS SEQRES 7 C 97 GLY HIS PHE VAL TYR PHE TYR ILE GLY PRO LEU ALA PHE SEQRES 8 C 97 LEU VAL PHE LYS THR ALA SEQRES 1 D 11 ASN TYR ALA GLU SER GLY ILE GLN THR ASP LEU FORMUL 5 HOH *217(H2 O) HELIX 1 1 THR A 17 TYR A 35 1 19 HELIX 2 2 LEU A 37 GLY A 54 1 18 HELIX 3 3 THR C 17 ASP C 33 1 17 HELIX 4 4 LEU C 37 GLY C 54 1 18 SHEET 1 A 8 ILE A 10 ILE A 16 0 SHEET 2 A 8 HIS A 75 ILE A 81 -1 O TYR A 78 N LYS A 12 SHEET 3 A 8 LEU A 84 LYS A 90 -1 O PHE A 86 N PHE A 79 SHEET 4 A 8 TRP A 57 HIS A 71 -1 N ILE A 60 O LEU A 87 SHEET 5 A 8 TRP C 57 GLU C 72 -1 O VAL C 61 N GLY A 66 SHEET 6 A 8 LEU C 84 LYS C 90 -1 O ALA C 85 N GLY C 62 SHEET 7 A 8 HIS C 75 ILE C 81 -1 N PHE C 79 O PHE C 86 SHEET 8 A 8 ILE C 10 ILE C 16 -1 N ASP C 15 O PHE C 76 SHEET 1 B 4 ALA B1118 GLN B1123 0 SHEET 2 B 4 TRP A 57 HIS A 71 -1 N HIS A 71 O ALA B1118 SHEET 3 B 4 TRP C 57 GLU C 72 -1 O VAL C 61 N GLY A 66 SHEET 4 B 4 TYR D1117 GLN D1123 -1 O ALA D1118 N HIS C 71 CISPEP 1 ASN A 55 THR A 56 0 3.28 CISPEP 2 ASN C 55 THR C 56 0 2.78 CRYST1 33.869 47.971 110.703 90.00 90.00 90.00 P 21 21 21 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 0.029526 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020846 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009033 0.00000