HEADER HYDROLASE 01-JUN-09 2WJY TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN NONSENSE MEDIATED DECAY TITLE 2 FACTORS UPF1 AND UPF2 ORTHORHOMBIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF NONSENSE TRANSCRIPTS 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914; COMPND 5 SYNONYM: UPF1, ATP-DEPENDENT HELICASE RENT1, NONSENSE MRNA REDUCING COMPND 6 FACTOR 1, UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG, NORF1, HUPF1; COMPND 7 EC: 3.6.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 STAR (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PCDF-DUET1 KEYWDS NONSENSE MEDIATED DECAY, ZINC-FINGER, ATP-BINDING, METAL-BINDING, KEYWDS 2 UPF2, UPF1, HELICASE, HYDROLASE, NONSENSE-MEDIATED MRNA DECAY, KEYWDS 3 PHOSPHOPROTEIN, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.CLERICI,A.MOURAO,I.GUTSCHE,N.H.GEHRING,M.W.HENTZE,A.KULOZIK, AUTHOR 2 J.KADLEC,M.SATTLER,S.CUSACK REVDAT 4 13-DEC-23 2WJY 1 REMARK LINK REVDAT 3 13-JUL-11 2WJY 1 VERSN REVDAT 2 25-AUG-09 2WJY 1 JRNL REVDAT 1 07-JUL-09 2WJY 0 JRNL AUTH M.CLERICI,A.MOURAO,I.GUTSCHE,N.H.GEHRING,M.W.HENTZE, JRNL AUTH 2 A.KULOZIK,J.KADLEC,M.SATTLER,S.CUSACK JRNL TITL UNUSUAL BIPARTITE MODE OF INTERACTION BETWEEN THE JRNL TITL 2 NONSENSE-MEDIATED DECAY FACTORS, UPF1 AND UPF2. JRNL REF EMBO J. V. 28 2293 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19556969 JRNL DOI 10.1038/EMBOJ.2009.175 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 42869 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2266 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3120 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6107 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : 0.38000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.308 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.680 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6326 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8570 ; 1.386 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 776 ; 6.408 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 285 ;35.747 ;24.386 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1126 ;17.786 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;19.173 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 955 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4721 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3888 ; 0.575 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6293 ; 1.139 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2438 ; 1.827 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2277 ; 3.083 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 116 A 279 REMARK 3 ORIGIN FOR THE GROUP (A): 59.3650 17.6390 15.3740 REMARK 3 T TENSOR REMARK 3 T11: 0.7949 T22: 0.7898 REMARK 3 T33: 0.3124 T12: 0.0264 REMARK 3 T13: 0.2273 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 5.7523 L22: 0.9599 REMARK 3 L33: 6.9806 L12: 0.1417 REMARK 3 L13: -4.6768 L23: 0.2814 REMARK 3 S TENSOR REMARK 3 S11: 0.1258 S12: 0.3385 S13: 0.1633 REMARK 3 S21: -0.2399 S22: -0.0788 S23: -0.2218 REMARK 3 S31: -0.2472 S32: 0.2875 S33: -0.0470 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 288 A 457 REMARK 3 ORIGIN FOR THE GROUP (A): 31.4420 37.5500 47.1300 REMARK 3 T TENSOR REMARK 3 T11: 0.1683 T22: 0.1853 REMARK 3 T33: 0.1781 T12: -0.0068 REMARK 3 T13: -0.0137 T23: 0.0695 REMARK 3 L TENSOR REMARK 3 L11: 1.6565 L22: 2.3377 REMARK 3 L33: 1.3581 L12: -0.8705 REMARK 3 L13: -0.4855 L23: 0.8236 REMARK 3 S TENSOR REMARK 3 S11: 0.0031 S12: 0.2082 S13: 0.2970 REMARK 3 S21: -0.2684 S22: -0.0142 S23: 0.1064 REMARK 3 S31: -0.1958 S32: -0.0334 S33: 0.0111 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 458 A 913 REMARK 3 ORIGIN FOR THE GROUP (A): 27.8700 23.8460 61.0440 REMARK 3 T TENSOR REMARK 3 T11: 0.0140 T22: 0.0471 REMARK 3 T33: 0.0746 T12: 0.0154 REMARK 3 T13: -0.0060 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 1.8390 L22: 0.9298 REMARK 3 L33: 1.1155 L12: 0.0902 REMARK 3 L13: -0.3117 L23: -0.0595 REMARK 3 S TENSOR REMARK 3 S11: 0.0172 S12: 0.1166 S13: 0.0994 REMARK 3 S21: -0.0285 S22: 0.0223 S23: 0.0678 REMARK 3 S31: -0.0984 S32: -0.0567 S33: -0.0395 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES RESIDUAL ONLY REMARK 4 REMARK 4 2WJY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1290040020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45136 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.710 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 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) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.78 REMARK 200 R MERGE FOR SHELL (I) : 0.77000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: PDB ENTRIES 2GK7, 2IYK REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULPHATE, 100 MM MES PH REMARK 280 6, 10% DIOXANE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.45500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.57000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 155.63500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.45500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.57000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 155.63500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.45500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.57000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 155.63500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.45500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.57000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 155.63500 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: PQS 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 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 THR A 115 REMARK 465 ALA A 199 REMARK 465 LYS A 200 REMARK 465 ALA A 201 REMARK 465 ASP A 202 REMARK 465 SER A 203 REMARK 465 LEU A 219 REMARK 465 LYS A 220 REMARK 465 ASP A 221 REMARK 465 ILE A 222 REMARK 465 ASN A 223 REMARK 465 TRP A 224 REMARK 465 ASP A 225 REMARK 465 SER A 226 REMARK 465 SER A 227 REMARK 465 GLN A 228 REMARK 465 LEU A 280 REMARK 465 GLU A 281 REMARK 465 LYS A 282 REMARK 465 PRO A 283 REMARK 465 GLY A 284 REMARK 465 VAL A 285 REMARK 465 ASP A 286 REMARK 465 GLU A 287 REMARK 465 ASP A 353 REMARK 465 MET A 354 REMARK 465 SER A 914 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 117 -168.91 -68.06 REMARK 500 HIS A 129 27.32 -142.07 REMARK 500 LYS A 166 -21.47 -155.47 REMARK 500 THR A 325 127.44 -36.75 REMARK 500 ASN A 328 69.27 -111.92 REMARK 500 ASP A 385 -153.66 -154.64 REMARK 500 PRO A 402 46.18 -66.81 REMARK 500 VAL A 403 -35.85 -35.79 REMARK 500 THR A 406 -33.88 -134.18 REMARK 500 ASN A 408 42.02 71.53 REMARK 500 CYS A 457 149.42 -173.79 REMARK 500 ASN A 514 40.20 -99.93 REMARK 500 ASP A 582 43.92 -80.24 REMARK 500 THR A 584 -39.19 -136.44 REMARK 500 LYS A 627 -0.02 75.25 REMARK 500 ASP A 662 114.32 -160.22 REMARK 500 GLN A 665 -150.93 -119.73 REMARK 500 GLU A 718 42.24 38.74 REMARK 500 VAL A 842 -57.18 71.10 REMARK 500 LYS A 881 57.28 -93.78 REMARK 500 GLN A 882 117.50 -177.58 REMARK 500 PRO A 883 114.53 -29.65 REMARK 500 LEU A 884 -16.38 78.68 REMARK 500 ASN A 905 64.20 -150.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 SULPHATE ION (SO4): FROM CRSYTALLISATION MEDIUM REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 123 SG REMARK 620 2 CYS A 145 SG 111.3 REMARK 620 3 HIS A 155 ND1 126.2 90.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 137 SG REMARK 620 2 SER A 140 OG 130.8 REMARK 620 3 HIS A 159 NE2 104.2 86.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 186 SG REMARK 620 2 CYS A 213 SG 122.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 990 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 991 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 992 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 993 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 994 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 995 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 996 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 997 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WJV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN NONSENSE MEDIATED REMARK 900 DECAY FACTORS UPF1 AND UPF2 REMARK 900 RELATED ID: 2IYK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UPF2-INTERACTING DOMAIN OF NONSENSE REMARK 900 MEDIATED MRNA DECAY FACTOR UPF1 DBREF 2WJY A 115 914 UNP Q92900 RENT1_HUMAN 115 914 SEQRES 1 A 800 THR LYS ASP LEU PRO ILE HIS ALA CYS SER TYR CYS GLY SEQRES 2 A 800 ILE HIS ASP PRO ALA CYS VAL VAL TYR CYS ASN THR SER SEQRES 3 A 800 LYS LYS TRP PHE CYS ASN GLY ARG GLY ASN THR SER GLY SEQRES 4 A 800 SER HIS ILE VAL ASN HIS LEU VAL ARG ALA LYS CYS LYS SEQRES 5 A 800 GLU VAL THR LEU HIS LYS ASP GLY PRO LEU GLY GLU THR SEQRES 6 A 800 VAL LEU GLU CYS TYR ASN CYS GLY CYS ARG ASN VAL PHE SEQRES 7 A 800 LEU LEU GLY PHE ILE PRO ALA LYS ALA ASP SER VAL VAL SEQRES 8 A 800 VAL LEU LEU CYS ARG GLN PRO CYS ALA SER GLN SER SER SEQRES 9 A 800 LEU LYS ASP ILE ASN TRP ASP SER SER GLN TRP GLN PRO SEQRES 10 A 800 LEU ILE GLN ASP ARG CYS PHE LEU SER TRP LEU VAL LYS SEQRES 11 A 800 ILE PRO SER GLU GLN GLU GLN LEU ARG ALA ARG GLN ILE SEQRES 12 A 800 THR ALA GLN GLN ILE ASN LYS LEU GLU GLU LEU TRP LYS SEQRES 13 A 800 GLU ASN PRO SER ALA THR LEU GLU ASP LEU GLU LYS PRO SEQRES 14 A 800 GLY VAL ASP GLU GLU PRO GLN HIS VAL LEU LEU ARG TYR SEQRES 15 A 800 GLU ASP ALA TYR GLN TYR GLN ASN ILE PHE GLY PRO LEU SEQRES 16 A 800 VAL LYS LEU GLU ALA ASP TYR ASP LYS LYS LEU LYS GLU SEQRES 17 A 800 SER GLN THR GLN ASP ASN ILE THR VAL ARG TRP ASP LEU SEQRES 18 A 800 GLY LEU ASN LYS LYS ARG ILE ALA TYR PHE THR LEU PRO SEQRES 19 A 800 LYS THR ASP SER ASP MET ARG LEU MET GLN GLY ASP GLU SEQRES 20 A 800 ILE CYS LEU ARG TYR LYS GLY ASP LEU ALA PRO LEU TRP SEQRES 21 A 800 LYS GLY ILE GLY HIS VAL ILE LYS VAL PRO ASP ASN TYR SEQRES 22 A 800 GLY ASP GLU ILE ALA ILE GLU LEU ARG SER SER VAL GLY SEQRES 23 A 800 ALA PRO VAL GLU VAL THR HIS ASN PHE GLN VAL ASP PHE SEQRES 24 A 800 VAL TRP LYS SER THR SER PHE ASP ARG MET GLN SER ALA SEQRES 25 A 800 LEU LYS THR PHE ALA VAL ASP GLU THR SER VAL SER GLY SEQRES 26 A 800 TYR ILE TYR HIS LYS LEU LEU GLY HIS GLU VAL GLU ASP SEQRES 27 A 800 VAL ILE ILE LYS CYS GLN LEU PRO LYS ARG PHE THR ALA SEQRES 28 A 800 GLN GLY LEU PRO ASP LEU ASN HIS SER GLN VAL TYR ALA SEQRES 29 A 800 VAL LYS THR VAL LEU GLN ARG PRO LEU SER LEU ILE GLN SEQRES 30 A 800 GLY PRO PRO GLY THR GLY LYS THR VAL THR SER ALA THR SEQRES 31 A 800 ILE VAL TYR HIS LEU ALA ARG GLN GLY ASN GLY PRO VAL SEQRES 32 A 800 LEU VAL CYS ALA PRO SER ASN ILE ALA VAL ASP GLN LEU SEQRES 33 A 800 THR GLU LYS ILE HIS GLN THR GLY LEU LYS VAL VAL ARG SEQRES 34 A 800 LEU CYS ALA LYS SER ARG GLU ALA ILE ASP SER PRO VAL SEQRES 35 A 800 SER PHE LEU ALA LEU HIS ASN GLN ILE ARG ASN MET ASP SEQRES 36 A 800 SER MET PRO GLU LEU GLN LYS LEU GLN GLN LEU LYS ASP SEQRES 37 A 800 GLU THR GLY GLU LEU SER SER ALA ASP GLU LYS ARG TYR SEQRES 38 A 800 ARG ALA LEU LYS ARG THR ALA GLU ARG GLU LEU LEU MET SEQRES 39 A 800 ASN ALA ASP VAL ILE CYS CYS THR CYS VAL GLY ALA GLY SEQRES 40 A 800 ASP PRO ARG LEU ALA LYS MET GLN PHE ARG SER ILE LEU SEQRES 41 A 800 ILE ASP GLU SER THR GLN ALA THR GLU PRO GLU CYS MET SEQRES 42 A 800 VAL PRO VAL VAL LEU GLY ALA LYS GLN LEU ILE LEU VAL SEQRES 43 A 800 GLY ASP HIS CYS GLN LEU GLY PRO VAL VAL MET CYS LYS SEQRES 44 A 800 LYS ALA ALA LYS ALA GLY LEU SER GLN SER LEU PHE GLU SEQRES 45 A 800 ARG LEU VAL VAL LEU GLY ILE ARG PRO ILE ARG LEU GLN SEQRES 46 A 800 VAL GLN TYR ARG MET HIS PRO ALA LEU SER ALA PHE PRO SEQRES 47 A 800 SER ASN ILE PHE TYR GLU GLY SER LEU GLN ASN GLY VAL SEQRES 48 A 800 THR ALA ALA ASP ARG VAL LYS LYS GLY PHE ASP PHE GLN SEQRES 49 A 800 TRP PRO GLN PRO ASP LYS PRO MET PHE PHE TYR VAL THR SEQRES 50 A 800 GLN GLY GLN GLU GLU ILE ALA SER SER GLY THR SER TYR SEQRES 51 A 800 LEU ASN ARG THR GLU ALA ALA ASN VAL GLU LYS ILE THR SEQRES 52 A 800 THR LYS LEU LEU LYS ALA GLY ALA LYS PRO ASP GLN ILE SEQRES 53 A 800 GLY ILE ILE THR PRO TYR GLU GLY GLN ARG SER TYR LEU SEQRES 54 A 800 VAL GLN TYR MET GLN PHE SER GLY SER LEU HIS THR LYS SEQRES 55 A 800 LEU TYR GLN GLU VAL GLU ILE ALA SER VAL ASP ALA PHE SEQRES 56 A 800 GLN GLY ARG GLU LYS ASP PHE ILE ILE LEU SER CYS VAL SEQRES 57 A 800 ARG ALA ASN GLU HIS GLN GLY ILE GLY PHE LEU ASN ASP SEQRES 58 A 800 PRO ARG ARG LEU ASN VAL ALA LEU THR ARG ALA ARG TYR SEQRES 59 A 800 GLY VAL ILE ILE VAL GLY ASN PRO LYS ALA LEU SER LYS SEQRES 60 A 800 GLN PRO LEU TRP ASN HIS LEU LEU ASN TYR TYR LYS GLU SEQRES 61 A 800 GLN LYS VAL LEU VAL GLU GLY PRO LEU ASN ASN LEU ARG SEQRES 62 A 800 GLU SER LEU MET GLN PHE SER HET ZN A 1 1 HET ZN A 2 1 HET ZN A 3 1 HET SO4 A 990 5 HET SO4 A 991 5 HET SO4 A 992 5 HET SO4 A 993 5 HET SO4 A 994 5 HET SO4 A 995 5 HET SO4 A 996 5 HET SO4 A 997 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 SO4 8(O4 S 2-) FORMUL 13 HOH *254(H2 O) HELIX 1 1 ASP A 130 ALA A 132 5 3 HELIX 2 2 SER A 154 LYS A 164 1 11 HELIX 3 3 SER A 247 ALA A 254 1 8 HELIX 4 4 THR A 258 LYS A 270 1 13 HELIX 5 5 ASP A 298 GLN A 324 1 27 HELIX 6 6 SER A 417 ASP A 433 1 17 HELIX 7 7 SER A 438 LEU A 446 1 9 HELIX 8 8 ASN A 472 GLN A 484 1 13 HELIX 9 9 GLY A 497 ARG A 511 1 15 HELIX 10 10 SER A 523 GLN A 536 1 14 HELIX 11 11 ALA A 546 ILE A 552 5 7 HELIX 12 12 VAL A 556 LEU A 559 5 4 HELIX 13 13 ALA A 560 ASN A 567 1 8 HELIX 14 14 MET A 571 ASP A 582 1 12 HELIX 15 15 SER A 588 ALA A 610 1 23 HELIX 16 16 VAL A 618 ASP A 622 5 5 HELIX 17 17 GLU A 637 ALA A 641 5 5 HELIX 18 18 THR A 642 VAL A 651 1 10 HELIX 19 19 CYS A 672 ALA A 678 1 7 HELIX 20 20 SER A 683 LEU A 691 1 9 HELIX 21 21 HIS A 705 TYR A 717 1 13 HELIX 22 22 ALA A 727 VAL A 731 5 5 HELIX 23 23 ASN A 766 ALA A 783 1 18 HELIX 24 24 LYS A 786 ASP A 788 5 3 HELIX 25 25 TYR A 796 GLY A 811 1 16 HELIX 26 26 HIS A 814 GLU A 820 1 7 HELIX 27 27 SER A 825 GLN A 830 5 6 HELIX 28 28 ILE A 850 ASN A 854 5 5 HELIX 29 29 ASP A 855 THR A 864 1 10 HELIX 30 30 ASN A 875 SER A 880 1 6 HELIX 31 31 GLN A 882 GLN A 895 1 14 HELIX 32 32 PRO A 902 LEU A 906 5 5 SHEET 1 AA 3 LYS A 142 CYS A 145 0 SHEET 2 AA 3 VAL A 134 CYS A 137 -1 O VAL A 135 N PHE A 144 SHEET 3 AA 3 VAL A 168 LEU A 170 -1 O THR A 169 N TYR A 136 SHEET 1 AB 3 VAL A 206 LEU A 207 0 SHEET 2 AB 3 GLY A 195 ILE A 197 -1 O ILE A 197 N VAL A 206 SHEET 3 AB 3 GLN A 230 PRO A 231 -1 O GLN A 230 N PHE A 196 SHEET 1 AC 7 GLN A 326 ILE A 329 0 SHEET 2 AC 7 PHE A 409 PHE A 413 -1 O PHE A 409 N ILE A 329 SHEET 3 AC 7 GLU A 361 TYR A 366 -1 O CYS A 363 N ASP A 412 SHEET 4 AC 7 TRP A 374 LYS A 382 -1 O TRP A 374 N TYR A 366 SHEET 5 AC 7 ILE A 391 LEU A 395 -1 O ALA A 392 N ILE A 381 SHEET 6 AC 7 ARG A 341 PHE A 345 -1 O ARG A 341 N LEU A 395 SHEET 7 AC 7 ARG A 332 LEU A 335 -1 O ARG A 332 N TYR A 344 SHEET 1 AD 7 VAL A 541 ARG A 543 0 SHEET 2 AD 7 VAL A 612 THR A 616 1 O VAL A 612 N VAL A 542 SHEET 3 AD 7 VAL A 517 ALA A 521 1 O VAL A 517 N ILE A 613 SHEET 4 AD 7 SER A 632 ILE A 635 1 O SER A 632 N LEU A 518 SHEET 5 AD 7 GLN A 656 GLY A 661 1 O GLN A 656 N ILE A 633 SHEET 6 AD 7 LEU A 487 GLN A 491 1 O SER A 488 N LEU A 659 SHEET 7 AD 7 ILE A 696 ARG A 697 1 O ILE A 696 N GLN A 491 SHEET 1 AE 2 VAL A 700 GLN A 701 0 SHEET 2 AE 2 GLN A 722 ASN A 723 1 O GLN A 722 N GLN A 701 SHEET 1 AF 7 GLU A 822 ALA A 824 0 SHEET 2 AF 7 ILE A 790 ILE A 793 1 O ILE A 790 N GLU A 822 SHEET 3 AF 7 LYS A 834 SER A 840 1 O PHE A 836 N GLY A 791 SHEET 4 AF 7 ALA A 866 GLY A 874 1 N ARG A 867 O LYS A 834 SHEET 5 AF 7 MET A 746 VAL A 750 1 O PHE A 747 N ILE A 872 SHEET 6 AF 7 LEU A 898 GLU A 900 1 O VAL A 899 N VAL A 750 SHEET 7 AF 7 ARG A 907 GLU A 908 -1 O ARG A 907 N GLU A 900 SHEET 1 AG 2 GLU A 756 ILE A 757 0 SHEET 2 AG 2 TYR A 764 LEU A 765 -1 O LEU A 765 N GLU A 756 LINK ZN ZN A 1 SG CYS A 123 1555 1555 2.25 LINK ZN ZN A 1 SG CYS A 145 1555 1555 2.27 LINK ZN ZN A 1 ND1 HIS A 155 1555 1555 2.07 LINK ZN ZN A 2 SG CYS A 137 1555 1555 1.74 LINK ZN ZN A 2 OG SER A 140 1555 1555 2.31 LINK ZN ZN A 2 NE2 HIS A 159 1555 1555 2.49 LINK ZN ZN A 3 SG CYS A 186 1555 1555 1.96 LINK ZN ZN A 3 SG CYS A 213 1555 1555 2.46 CISPEP 1 GLN A 211 PRO A 212 0 -0.96 SITE 1 AC1 4 CYS A 123 CYS A 126 CYS A 145 HIS A 155 SITE 1 AC2 4 CYS A 137 SER A 140 HIS A 159 CYS A 165 SITE 1 AC3 4 CYS A 183 CYS A 186 CYS A 209 CYS A 213 SITE 1 AC4 10 PRO A 494 GLY A 495 ARG A 703 GLY A 831 SITE 2 AC4 10 ARG A 865 HOH A2091 HOH A2244 HOH A2245 SITE 3 AC4 10 HOH A2246 HOH A2247 SITE 1 AC5 6 TYR A 764 ARG A 843 HIS A 847 GLN A 848 SITE 2 AC5 6 GLY A 849 HOH A2206 SITE 1 AC6 2 ARG A 594 SER A 759 SITE 1 AC7 3 ARG A 832 HOH A2248 HOH A2250 SITE 1 AC8 4 ASN A 472 HIS A 473 GLN A 722 HOH A2081 SITE 1 AC9 5 ARG A 462 PHE A 463 THR A 464 VAL A 476 SITE 2 AC9 5 HOH A2252 SITE 1 BC1 8 THR A 794 PRO A 795 SER A 825 VAL A 826 SITE 2 BC1 8 GLY A 851 PHE A 852 HOH A2253 HOH A2254 SITE 1 BC2 2 LEU A 320 SER A 323 CRYST1 64.910 129.140 311.270 90.00 90.00 90.00 I 2 2 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 0.015406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003213 0.00000