HEADER TRANSPORT PROTEIN 15-MAR-13 4JNU TITLE CRYSTAL STRUCTURE OF THE HUMAN NUP57CCS3* COILED-COIL SEGMENT, SPACE TITLE 2 GROUP P21 CAVEAT 4JNU RESIDUES A LEU 489 AND A VAL 490 (CONFORMATION B) ARE NOT CAVEAT 2 4JNU PROPERLY LINKED. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPORIN P54; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 453-491; COMPND 5 SYNONYM: NUP54, 54 KDA NUCLEOPORIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUP54; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOCYTOPLASMIC TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.STUWE,C.J.BLEY,D.J.MAYO,A.HOELZ REVDAT 4 28-FEB-24 4JNU 1 SEQADV REVDAT 3 03-FEB-16 4JNU 1 JRNL REVDAT 2 02-SEP-15 4JNU 1 TITLE REVDAT 1 17-SEP-14 4JNU 0 JRNL AUTH T.STUWE,C.J.BLEY,K.THIERBACH,S.PETROVIC,S.SCHILBACH, JRNL AUTH 2 D.J.MAYO,T.PERRICHES,E.J.RUNDLET,Y.E.JEON,L.N.COLLINS, JRNL AUTH 3 F.M.HUBER,D.H.LIN,M.PADUCH,A.KOIDE,V.LU,J.FISCHER,E.HURT, JRNL AUTH 4 S.KOIDE,A.A.KOSSIAKOFF,A.HOELZ JRNL TITL ARCHITECTURE OF THE FUNGAL NUCLEAR PORE INNER RING COMPLEX. JRNL REF SCIENCE V. 350 56 2015 JRNL REFN ISSN 0036-8075 JRNL PMID 26316600 JRNL DOI 10.1126/SCIENCE.AAC9176 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 26274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.570 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 19.9474 - 3.4760 1.00 1857 152 0.1825 0.2171 REMARK 3 2 3.4760 - 2.7613 1.00 1807 147 0.1931 0.2218 REMARK 3 3 2.7613 - 2.4130 1.00 1787 149 0.1743 0.2258 REMARK 3 4 2.4130 - 2.1926 1.00 1807 144 0.1562 0.1953 REMARK 3 5 2.1926 - 2.0357 1.00 1808 148 0.1607 0.1879 REMARK 3 6 2.0357 - 1.9157 1.00 1783 145 0.1749 0.2035 REMARK 3 7 1.9157 - 1.8199 1.00 1780 145 0.1908 0.2371 REMARK 3 8 1.8199 - 1.7407 1.00 1784 148 0.1949 0.2137 REMARK 3 9 1.7407 - 1.6737 1.00 1771 150 0.1965 0.2222 REMARK 3 10 1.6737 - 1.6160 1.00 1814 140 0.1925 0.2348 REMARK 3 11 1.6160 - 1.5655 0.99 1773 147 0.2031 0.2237 REMARK 3 12 1.5655 - 1.5207 0.94 1655 136 0.2071 0.2612 REMARK 3 13 1.5207 - 1.4807 0.86 1522 127 0.2203 0.2661 REMARK 3 14 1.4807 - 1.4450 0.74 1336 112 0.2646 0.2784 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.87 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 : 0.007 1486 REMARK 3 ANGLE : 1.004 2010 REMARK 3 CHIRALITY : 0.054 234 REMARK 3 PLANARITY : 0.004 257 REMARK 3 DIHEDRAL : 15.831 594 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 4JNU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.445 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: PHENIX 1.8_1069 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH 5.3, 1.9 M REMARK 280 SODIUM FORMATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.56300 REMARK 290 SMTRY3 2 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: 7580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JNV RELATED DB: PDB REMARK 900 RELATED ID: 4JO7 RELATED DB: PDB REMARK 900 RELATED ID: 4JO9 RELATED DB: PDB REMARK 900 RELATED ID: 4JQ5 RELATED DB: PDB DBREF 4JNU A 452 490 UNP Q7Z3B4 NUP54_HUMAN 453 491 DBREF 4JNU B 453 491 UNP Q7Z3B4 NUP54_HUMAN 453 491 DBREF 4JNU C 454 492 UNP Q7Z3B4 NUP54_HUMAN 453 491 DBREF 4JNU D 453 491 UNP Q7Z3B4 NUP54_HUMAN 453 491 SEQADV 4JNU SER A 451 UNP Q7Z3B4 EXPRESSION TAG SEQADV 4JNU SER B 452 UNP Q7Z3B4 EXPRESSION TAG SEQADV 4JNU SER C 453 UNP Q7Z3B4 EXPRESSION TAG SEQADV 4JNU SER D 452 UNP Q7Z3B4 EXPRESSION TAG SEQRES 1 A 40 SER TYR TYR ILE ASP ALA ASP LEU LEU ARG GLU ILE LYS SEQRES 2 A 40 GLN HIS LEU LYS GLN GLN GLN GLU GLY LEU SER HIS LEU SEQRES 3 A 40 ILE SER ILE ILE LYS ASP ASP LEU GLU ASP ILE LYS LEU SEQRES 4 A 40 VAL SEQRES 1 B 40 SER TYR TYR ILE ASP ALA ASP LEU LEU ARG GLU ILE LYS SEQRES 2 B 40 GLN HIS LEU LYS GLN GLN GLN GLU GLY LEU SER HIS LEU SEQRES 3 B 40 ILE SER ILE ILE LYS ASP ASP LEU GLU ASP ILE LYS LEU SEQRES 4 B 40 VAL SEQRES 1 C 40 SER TYR TYR ILE ASP ALA ASP LEU LEU ARG GLU ILE LYS SEQRES 2 C 40 GLN HIS LEU LYS GLN GLN GLN GLU GLY LEU SER HIS LEU SEQRES 3 C 40 ILE SER ILE ILE LYS ASP ASP LEU GLU ASP ILE LYS LEU SEQRES 4 C 40 VAL SEQRES 1 D 40 SER TYR TYR ILE ASP ALA ASP LEU LEU ARG GLU ILE LYS SEQRES 2 D 40 GLN HIS LEU LYS GLN GLN GLN GLU GLY LEU SER HIS LEU SEQRES 3 D 40 ILE SER ILE ILE LYS ASP ASP LEU GLU ASP ILE LYS LEU SEQRES 4 D 40 VAL FORMUL 5 HOH *131(H2 O) HELIX 1 1 ALA A 456 ILE A 487 1 32 HELIX 2 2 LYS A 488 VAL A 490 5 3 HELIX 3 3 ASP B 458 ILE B 488 1 31 HELIX 4 4 ASP C 457 LEU C 491 1 35 HELIX 5 5 ASP D 456 GLU D 486 1 31 SHEET 1 A 2 TYR A 453 ASP A 455 0 SHEET 2 A 2 TYR B 454 ASP B 456 -1 O ILE B 455 N ILE A 454 SHEET 1 B 2 TYR C 454 TYR C 455 0 SHEET 2 B 2 TYR D 453 TYR D 454 1 O TYR D 453 N TYR C 455 CRYST1 39.909 45.126 46.384 90.00 113.75 90.00 P 1 21 1 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 0.025057 0.000000 0.011026 0.00000 SCALE2 0.000000 0.022160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023554 0.00000