HEADER TRANSPORT PROTEIN 18-MAR-13 4JO9 TITLE CRYSTAL STRUCTURE OF THE HUMAN NUP49CCS2+3* NUP57CCS3* COMPLEX 1:2 TITLE 2 STOICHIOMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPORIN P54; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 453-491; COMPND 5 SYNONYM: NUP54, 54 KDA NUCLEOPORIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEOPORIN P58/P45; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 341-426; COMPND 11 SYNONYM: NUP58, NUCLEOPORIN-LIKE PROTEIN 1; COMPND 12 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; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: NUPL1, KIAA0410; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 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 4JO9 1 SEQADV REVDAT 3 03-FEB-16 4JO9 1 JRNL REVDAT 2 02-SEP-15 4JO9 1 TITLE REVDAT 1 17-SEP-14 4JO9 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 10891 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.251 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1092 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 47.7987 - 4.9964 1.00 1375 153 0.2530 0.3083 REMARK 3 2 4.9964 - 3.9664 1.00 1262 140 0.1959 0.2105 REMARK 3 3 3.9664 - 3.4652 1.00 1250 139 0.2228 0.2653 REMARK 3 4 3.4652 - 3.1484 1.00 1230 136 0.2672 0.3006 REMARK 3 5 3.1484 - 2.9228 0.99 1203 134 0.2715 0.3398 REMARK 3 6 2.9228 - 2.7505 0.99 1205 136 0.2875 0.3532 REMARK 3 7 2.7505 - 2.6128 0.99 1186 133 0.3092 0.3912 REMARK 3 8 2.6128 - 2.4990 0.90 1088 121 0.3481 0.4663 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.22 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 : 0.002 1356 REMARK 3 ANGLE : 0.437 1822 REMARK 3 CHIRALITY : 0.028 206 REMARK 3 PLANARITY : 0.001 234 REMARK 3 DIHEDRAL : 14.845 524 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 4JO9 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_1000078295. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 3.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0001 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11003 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.499 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 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) : 2.50 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 3.8, 0.07 M REMARK 280 CALCIUM CHLORIDE, VAPOR DIFFUSION, TEMPERATURE 294.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 95.58000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.79000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 143.37000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 95.58000 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 143.37000 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 47.79000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A 455 REMARK 465 TYR A 456 REMARK 465 SER B 326 REMARK 465 ALA B 327 REMARK 465 LEU C 493 REMARK 465 VAL C 494 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JNU RELATED DB: PDB REMARK 900 RELATED ID: 4JNV RELATED DB: PDB REMARK 900 RELATED ID: 4JO7 RELATED DB: PDB REMARK 900 RELATED ID: 4JQ5 RELATED DB: PDB DBREF 4JO9 A 456 494 UNP Q7Z3B4 NUP54_HUMAN 453 491 DBREF 4JO9 B 327 412 UNP Q9BVL2 NUPL1_HUMAN 341 426 DBREF 4JO9 C 456 494 UNP Q7Z3B4 NUP54_HUMAN 453 491 SEQADV 4JO9 SER A 455 UNP Q7Z3B4 EXPRESSION TAG SEQADV 4JO9 SER B 326 UNP Q9BVL2 EXPRESSION TAG SEQADV 4JO9 SER C 455 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 87 SER ALA PRO ALA ASP TYR PHE ARG ILE LEU VAL GLN GLN SEQRES 2 B 87 PHE GLU VAL GLN LEU GLN GLN TYR ARG GLN GLN ILE GLU SEQRES 3 B 87 GLU LEU GLU ASN HIS LEU ALA THR GLN ALA ASN ASN SER SEQRES 4 B 87 HIS ILE THR PRO GLN ASP LEU SER MET ALA MET GLN LYS SEQRES 5 B 87 ILE TYR GLN THR PHE VAL ALA LEU ALA ALA GLN LEU GLN SEQRES 6 B 87 SER ILE HIS GLU ASN VAL LYS VAL LEU LYS GLU GLN TYR SEQRES 7 B 87 LEU GLY TYR ARG LYS MET PHE LEU GLY 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 FORMUL 4 HOH *17(H2 O) HELIX 1 1 ASP A 459 VAL A 494 1 36 HELIX 2 2 ALA B 329 THR B 359 1 31 HELIX 3 3 THR B 359 SER B 364 1 6 HELIX 4 4 THR B 367 LEU B 411 1 45 HELIX 5 5 ASP C 459 GLN C 473 1 15 HELIX 6 6 GLY C 476 LYS C 492 1 17 CISPEP 1 TYR A 457 ILE A 458 0 4.10 CRYST1 55.483 55.483 191.160 90.00 90.00 90.00 P 41 2 2 16 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 0.018024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005231 0.00000