HEADER HYDROLASE/RNA 26-NOV-10 2XZO TITLE UPF1 HELICASE - RNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF NONSENSE TRANSCRIPTS 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HELICASE DOMAIN, RESIDUES 295-914; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE RENT1, NONSENSE MRNA REDUCING FACTOR COMPND 6 1, NORF1, UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG, HUPF1, UP FRAMESHIFT COMPND 7 FACTOR 1; COMPND 8 EC: 3.6.4.13; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'; COMPND 12 CHAIN: D; COMPND 13 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(DE3) GOLD PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-RNA COMPLEX, NMD, RNA DEGRADATION, ALLOSTERIC REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR S.CHAKRABARTI,U.JAYACHANDRAN,F.BONNEAU,F.FIORINI,C.BASQUIN,S.DOMCKE, AUTHOR 2 H.LE HIR,E.CONTI REVDAT 3 20-DEC-23 2XZO 1 REMARK REVDAT 2 12-JUL-17 2XZO 1 REVDAT 1 30-MAR-11 2XZO 0 JRNL AUTH S.CHAKRABARTI,U.JAYACHANDRAN,F.BONNEAU,F.FIORINI,C.BASQUIN, JRNL AUTH 2 S.DOMCKE,H.LE HIR,E.CONTI JRNL TITL MOLECULAR MECHANISMS FOR THE RNA-DEPENDENT ATPASE ACTIVITY JRNL TITL 2 OF UPF1 AND ITS REGULATION BY UPF2. JRNL REF MOL.CELL V. 41 693 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 21419344 JRNL DOI 10.1016/J.MOLCEL.2011.02.010 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1774 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 49.1947 - 5.1590 1.00 3553 192 0.1886 0.2099 REMARK 3 2 5.1590 - 4.0955 1.00 3403 198 0.1486 0.1890 REMARK 3 3 4.0955 - 3.5780 1.00 3381 184 0.1673 0.2111 REMARK 3 4 3.5780 - 3.2509 1.00 3359 183 0.1959 0.2272 REMARK 3 5 3.2509 - 3.0179 1.00 3358 171 0.1987 0.2351 REMARK 3 6 3.0179 - 2.8400 1.00 3302 173 0.2065 0.2686 REMARK 3 7 2.8400 - 2.6978 1.00 3379 154 0.2110 0.2680 REMARK 3 8 2.6978 - 2.5804 1.00 3297 185 0.2365 0.3122 REMARK 3 9 2.5804 - 2.4810 1.00 3327 162 0.2827 0.3551 REMARK 3 10 2.4810 - 2.3954 0.98 3253 172 0.3029 0.3396 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 : 0.30 REMARK 3 B_SOL : 25.94 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16090 REMARK 3 B22 (A**2) : -0.85440 REMARK 3 B33 (A**2) : 1.01540 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 : 0.007 4908 REMARK 3 ANGLE : 1.024 6694 REMARK 3 CHIRALITY : 0.065 778 REMARK 3 PLANARITY : 0.005 837 REMARK 3 DIHEDRAL : 13.890 1795 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: RESIDUES 349-354 ARE DISORDERED. REMARK 3 RESIDUES 582-585 ARE DISORDERED REMARK 4 REMARK 4 2XZO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290046396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : LN2-COOLED DYNAMICALLY BENDABLE REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35441 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 49.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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 ENTRY 2WJV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH 4.6, 20 MM REMARK 280 CACL2, 15% MPD 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 38.53300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.16000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.94800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.16000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.53300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.94800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 LYS A 349 REMARK 465 THR A 350 REMARK 465 ASP A 351 REMARK 465 SER A 352 REMARK 465 ASP A 353 REMARK 465 MET A 354 REMARK 465 ASP A 582 REMARK 465 GLU A 583 REMARK 465 THR A 584 REMARK 465 GLY A 585 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 GLU A 297 CD OE1 OE2 REMARK 470 GLN A 326 CG CD OE1 NE2 REMARK 470 LYS A 339 CG CD CE NZ REMARK 470 LYS A 340 CE NZ REMARK 470 ARG A 355 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 367 CE NZ REMARK 470 LYS A 375 CE NZ REMARK 470 ARG A 396 CD NE CZ NH1 NH2 REMARK 470 VAL A 399 CG1 CG2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 GLU A 449 CD OE1 OE2 REMARK 470 GLU A 451 CD OE1 OE2 REMARK 470 LYS A 456 CE NZ REMARK 470 GLN A 458 CG CD OE1 NE2 REMARK 470 GLN A 466 CD OE1 NE2 REMARK 470 GLU A 532 CD OE1 OE2 REMARK 470 LYS A 547 CD CE NZ REMARK 470 ARG A 566 NE CZ NH1 NH2 REMARK 470 ASP A 569 OD1 OD2 REMARK 470 MET A 571 CG SD CE REMARK 470 GLU A 573 CG CD OE1 OE2 REMARK 470 GLN A 575 CG CD OE1 NE2 REMARK 470 LYS A 576 CE NZ REMARK 470 LEU A 577 CG CD1 CD2 REMARK 470 GLN A 578 CG CD OE1 NE2 REMARK 470 GLN A 579 CG CD OE1 NE2 REMARK 470 LEU A 580 CG CD1 CD2 REMARK 470 LYS A 581 CE NZ REMARK 470 GLU A 586 CG CD OE1 OE2 REMARK 470 LEU A 587 CG CD1 CD2 REMARK 470 SER A 588 OG REMARK 470 SER A 589 OG REMARK 470 ASP A 591 CG OD1 OD2 REMARK 470 LYS A 593 CG CD CE NZ REMARK 470 ARG A 594 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 598 CG CD1 CD2 REMARK 470 ARG A 600 CG CD NE CZ NH1 NH2 REMARK 470 THR A 601 OG1 CG2 REMARK 470 ARG A 604 CZ NH1 NH2 REMARK 470 GLU A 605 CD OE1 OE2 REMARK 470 LYS A 627 CG CD CE NZ REMARK 470 ARG A 631 CZ NH1 NH2 REMARK 470 LYS A 673 CD CE NZ REMARK 470 LYS A 677 CD CE NZ REMARK 470 ARG A 694 CD NE CZ NH1 NH2 REMARK 470 LYS A 732 CE NZ REMARK 470 LYS A 733 CG CD CE NZ REMARK 470 ASP A 736 CG OD1 OD2 REMARK 470 GLN A 738 CG CD OE1 NE2 REMARK 470 LYS A 744 CE NZ REMARK 470 GLN A 754 OE1 NE2 REMARK 470 SER A 759 OG REMARK 470 GLU A 774 CD OE1 OE2 REMARK 470 LYS A 779 CD CE NZ REMARK 470 LYS A 782 CD CE NZ REMARK 470 LYS A 786 NZ REMARK 470 SER A 801 OG REMARK 470 GLN A 805 CD OE1 NE2 REMARK 470 LYS A 816 CE NZ REMARK 470 GLU A 846 CG CD OE1 OE2 REMARK 470 HIS A 847 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 848 CD OE1 NE2 REMARK 470 LYS A 877 CG CD CE NZ REMARK 470 SER A 880 OG REMARK 470 LYS A 881 NZ REMARK 470 LYS A 893 CE NZ REMARK 470 GLU A 894 CG CD OE1 OE2 REMARK 470 LYS A 896 CE NZ REMARK 470 LEU A 910 CG CD1 CD2 REMARK 470 MET A 911 CG SD CE REMARK 470 GLN A 912 CG CD OE1 NE2 REMARK 470 SER A 914 OG REMARK 470 U D 7 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U D 7 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U D 7 C5 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O1B ADP A 1004 AL ALF A 1005 1.96 REMARK 500 AL ALF A 1005 O HOH A 1104 2.06 REMARK 500 REMARK 500 REMARK: NULL 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 327 31.15 -80.65 REMARK 500 ASP A 385 -148.83 -157.69 REMARK 500 ASN A 408 33.27 81.29 REMARK 500 LYS A 456 59.85 -94.36 REMARK 500 ASN A 567 30.89 -95.77 REMARK 500 ASP A 736 67.10 -110.60 REMARK 500 SER A 810 -154.49 -89.05 REMARK 500 SER A 812 142.64 -33.95 REMARK 500 VAL A 842 -63.85 69.90 REMARK 500 ALA A 844 97.47 -169.68 REMARK 500 HIS A 847 45.35 -154.34 REMARK 500 MET A 911 128.54 -35.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 1001 REMARK 610 1PE A 1002 REMARK 610 1PE A 1003 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 MG A1006 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 499 OG1 REMARK 620 2 ADP A1004 O2B 85.5 REMARK 620 3 HOH A1106 O 81.3 99.7 REMARK 620 4 HOH A1119 O 80.1 82.0 161.1 REMARK 620 5 HOH A1195 O 79.3 159.8 91.2 82.3 REMARK 620 N 1 2 3 4 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE B 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP E 480 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALF E 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 482 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 483 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: 2WJY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN NONSENSE MEDIATED REMARK 900 DECAY FACTORS UPF1 AND UPF2 ORTHORHOMBIC FORM 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 REMARK 900 RELATED ID: 2XZP RELATED DB: PDB REMARK 900 UPF1 HELICASE REMARK 900 RELATED ID: 2GJK RELATED DB: PDB REMARK 900 STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE HUMAN UPF1 HELICASE CORE REMARK 900 RELATED ID: 2GK7 RELATED DB: PDB REMARK 900 STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE HUMAN UPF1 HELICASE CORE REMARK 900 RELATED ID: 2GK6 RELATED DB: PDB REMARK 900 STRUCTURAL AND FUNCTIONAL INSIGHTS INTO THE HUMAN UPF1 HELICASE CORE DBREF 2XZO A 295 914 UNP Q92900 RENT1_HUMAN 295 914 DBREF 2XZO D 1 7 PDB 2XZO 2XZO 1 7 SEQADV 2XZO GLY A 292 UNP Q92900 EXPRESSION TAG SEQADV 2XZO HIS A 293 UNP Q92900 EXPRESSION TAG SEQADV 2XZO MET A 294 UNP Q92900 EXPRESSION TAG SEQRES 1 A 623 GLY HIS MET ARG TYR GLU ASP ALA TYR GLN TYR GLN ASN SEQRES 2 A 623 ILE PHE GLY PRO LEU VAL LYS LEU GLU ALA ASP TYR ASP SEQRES 3 A 623 LYS LYS LEU LYS GLU SER GLN THR GLN ASP ASN ILE THR SEQRES 4 A 623 VAL ARG TRP ASP LEU GLY LEU ASN LYS LYS ARG ILE ALA SEQRES 5 A 623 TYR PHE THR LEU PRO LYS THR ASP SER ASP MET ARG LEU SEQRES 6 A 623 MET GLN GLY ASP GLU ILE CYS LEU ARG TYR LYS GLY ASP SEQRES 7 A 623 LEU ALA PRO LEU TRP LYS GLY ILE GLY HIS VAL ILE LYS SEQRES 8 A 623 VAL PRO ASP ASN TYR GLY ASP GLU ILE ALA ILE GLU LEU SEQRES 9 A 623 ARG SER SER VAL GLY ALA PRO VAL GLU VAL THR HIS ASN SEQRES 10 A 623 PHE GLN VAL ASP PHE VAL TRP LYS SER THR SER PHE ASP SEQRES 11 A 623 ARG MET GLN SER ALA LEU LYS THR PHE ALA VAL ASP GLU SEQRES 12 A 623 THR SER VAL SER GLY TYR ILE TYR HIS LYS LEU LEU GLY SEQRES 13 A 623 HIS GLU VAL GLU ASP VAL ILE ILE LYS CYS GLN LEU PRO SEQRES 14 A 623 LYS ARG PHE THR ALA GLN GLY LEU PRO ASP LEU ASN HIS SEQRES 15 A 623 SER GLN VAL TYR ALA VAL LYS THR VAL LEU GLN ARG PRO SEQRES 16 A 623 LEU SER LEU ILE GLN GLY PRO PRO GLY THR GLY LYS THR SEQRES 17 A 623 VAL THR SER ALA THR ILE VAL TYR HIS LEU ALA ARG GLN SEQRES 18 A 623 GLY ASN GLY PRO VAL LEU VAL CYS ALA PRO SER ASN ILE SEQRES 19 A 623 ALA VAL ASP GLN LEU THR GLU LYS ILE HIS GLN THR GLY SEQRES 20 A 623 LEU LYS VAL VAL ARG LEU CYS ALA LYS SER ARG GLU ALA SEQRES 21 A 623 ILE ASP SER PRO VAL SER PHE LEU ALA LEU HIS ASN GLN SEQRES 22 A 623 ILE ARG ASN MET ASP SER MET PRO GLU LEU GLN LYS LEU SEQRES 23 A 623 GLN GLN LEU LYS ASP GLU THR GLY GLU LEU SER SER ALA SEQRES 24 A 623 ASP GLU LYS ARG TYR ARG ALA LEU LYS ARG THR ALA GLU SEQRES 25 A 623 ARG GLU LEU LEU MET ASN ALA ASP VAL ILE CYS CYS THR SEQRES 26 A 623 CYS VAL GLY ALA GLY ASP PRO ARG LEU ALA LYS MET GLN SEQRES 27 A 623 PHE ARG SER ILE LEU ILE ASP GLU SER THR GLN ALA THR SEQRES 28 A 623 GLU PRO GLU CYS MET VAL PRO VAL VAL LEU GLY ALA LYS SEQRES 29 A 623 GLN LEU ILE LEU VAL GLY ASP HIS CYS GLN LEU GLY PRO SEQRES 30 A 623 VAL VAL MET CYS LYS LYS ALA ALA LYS ALA GLY LEU SER SEQRES 31 A 623 GLN SER LEU PHE GLU ARG LEU VAL VAL LEU GLY ILE ARG SEQRES 32 A 623 PRO ILE ARG LEU GLN VAL GLN TYR ARG MET HIS PRO ALA SEQRES 33 A 623 LEU SER ALA PHE PRO SER ASN ILE PHE TYR GLU GLY SER SEQRES 34 A 623 LEU GLN ASN GLY VAL THR ALA ALA ASP ARG VAL LYS LYS SEQRES 35 A 623 GLY PHE ASP PHE GLN TRP PRO GLN PRO ASP LYS PRO MET SEQRES 36 A 623 PHE PHE TYR VAL THR GLN GLY GLN GLU GLU ILE ALA SER SEQRES 37 A 623 SER GLY THR SER TYR LEU ASN ARG THR GLU ALA ALA ASN SEQRES 38 A 623 VAL GLU LYS ILE THR THR LYS LEU LEU LYS ALA GLY ALA SEQRES 39 A 623 LYS PRO ASP GLN ILE GLY ILE ILE THR PRO TYR GLU GLY SEQRES 40 A 623 GLN ARG SER TYR LEU VAL GLN TYR MET GLN PHE SER GLY SEQRES 41 A 623 SER LEU HIS THR LYS LEU TYR GLN GLU VAL GLU ILE ALA SEQRES 42 A 623 SER VAL ASP ALA PHE GLN GLY ARG GLU LYS ASP PHE ILE SEQRES 43 A 623 ILE LEU SER CYS VAL ARG ALA ASN GLU HIS GLN GLY ILE SEQRES 44 A 623 GLY PHE LEU ASN ASP PRO ARG ARG LEU ASN VAL ALA LEU SEQRES 45 A 623 THR ARG ALA ARG TYR GLY VAL ILE ILE VAL GLY ASN PRO SEQRES 46 A 623 LYS ALA LEU SER LYS GLN PRO LEU TRP ASN HIS LEU LEU SEQRES 47 A 623 ASN TYR TYR LYS GLU GLN LYS VAL LEU VAL GLU GLY PRO SEQRES 48 A 623 LEU ASN ASN LEU ARG GLU SER LEU MET GLN PHE SER SEQRES 1 D 7 U U U U U U U HET 1PE A1001 10 HET 1PE A1002 7 HET 1PE A1003 7 HET ADP A1004 27 HET ALF A1005 5 HET MG A1006 1 HET MG A1007 1 HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ALF TETRAFLUOROALUMINATE ION HETNAM MG MAGNESIUM ION HETSYN 1PE PEG400 FORMUL 3 1PE 3(C10 H22 O6) FORMUL 6 ADP C10 H15 N5 O10 P2 FORMUL 7 ALF AL F4 1- FORMUL 8 MG 2(MG 2+) FORMUL 10 HOH *125(H2 O) HELIX 1 1 ALA A 299 LYS A 321 1 23 HELIX 2 2 SER A 417 VAL A 432 1 16 HELIX 3 3 GLY A 439 LEU A 446 1 8 HELIX 4 4 HIS A 473 GLN A 484 1 12 HELIX 5 5 LYS A 498 GLN A 512 1 15 HELIX 6 6 ASN A 524 THR A 537 1 14 HELIX 7 7 SER A 557 LEU A 559 5 3 HELIX 8 8 LEU A 561 ASN A 567 1 7 HELIX 9 9 MET A 571 LEU A 580 1 10 HELIX 10 10 SER A 589 ASN A 609 1 21 HELIX 11 11 CYS A 617 GLY A 621 5 5 HELIX 12 12 SER A 638 GLN A 640 5 3 HELIX 13 13 GLU A 643 LEU A 652 1 10 HELIX 14 14 LYS A 673 ALA A 678 1 6 HELIX 15 15 LEU A 684 LEU A 691 1 8 HELIX 16 16 PRO A 706 PHE A 716 1 11 HELIX 17 17 ALA A 727 ASP A 729 5 3 HELIX 18 18 ARG A 767 ALA A 783 1 17 HELIX 19 19 PRO A 787 GLN A 789 5 3 HELIX 20 20 GLU A 797 PHE A 809 1 13 HELIX 21 21 THR A 815 GLU A 820 1 6 HELIX 22 22 VAL A 826 PHE A 829 1 4 HELIX 23 23 PHE A 852 ASN A 854 5 3 HELIX 24 24 PRO A 856 LEU A 863 1 8 HELIX 25 25 PRO A 876 LYS A 881 1 6 HELIX 26 26 PRO A 883 GLN A 895 1 13 SHEET 1 AA 6 ARG A 332 GLY A 336 0 SHEET 2 AA 6 LYS A 339 PHE A 345 -1 O ILE A 342 N ASP A 334 SHEET 3 AA 6 ILE A 391 LEU A 395 -1 O ILE A 391 N PHE A 345 SHEET 4 AA 6 TRP A 374 LYS A 382 -1 O HIS A 379 N GLU A 394 SHEET 5 AA 6 GLY A 359 TYR A 366 -1 O ILE A 362 N GLY A 378 SHEET 6 AA 6 PHE A 409 PHE A 413 -1 O GLN A 410 N ARG A 365 SHEET 1 AB 6 VAL A 541 LEU A 544 0 SHEET 2 AB 6 VAL A 612 THR A 616 1 O VAL A 612 N VAL A 542 SHEET 3 AB 6 VAL A 517 ALA A 521 1 O VAL A 517 N ILE A 613 SHEET 4 AB 6 SER A 632 ILE A 635 1 O SER A 632 N LEU A 518 SHEET 5 AB 6 GLN A 656 GLY A 661 1 O GLN A 656 N ILE A 633 SHEET 6 AB 6 LEU A 487 GLN A 491 1 O SER A 488 N LEU A 659 SHEET 1 AC 5 GLU A 822 SER A 825 0 SHEET 2 AC 5 ILE A 790 THR A 794 1 O ILE A 790 N GLU A 822 SHEET 3 AC 5 PHE A 836 SER A 840 1 O PHE A 836 N GLY A 791 SHEET 4 AC 5 GLY A 869 GLY A 874 1 O GLY A 869 N ILE A 837 SHEET 5 AC 5 MET A 746 VAL A 750 1 O PHE A 747 N ILE A 872 LINK OG1 THR A 499 MG MG A1006 1555 1555 2.31 LINK O MET A 807 MG MG A1007 1555 1555 2.90 LINK O2B ADP A1004 MG MG A1006 1555 1555 2.13 LINK MG MG A1006 O HOH A1106 1555 1555 2.23 LINK MG MG A1006 O HOH A1119 1555 1555 2.38 LINK MG MG A1006 O HOH A1195 1555 1555 2.28 CISPEP 1 GLY A 292 HIS A 293 0 6.55 CISPEP 2 VAL A 399 GLY A 400 0 0.36 CISPEP 3 ASP A 569 SER A 570 0 -8.24 SITE 1 AC1 8 ASN A 472 HIS A 473 SER A 474 THR A 496 SITE 2 AC1 8 LEU A 698 GLN A 699 VAL A 700 TYR A 702 SITE 1 AC2 5 ARG A 462 THR A 464 ALA A 465 GLN A 466 SITE 2 AC2 5 HOH A1189 SITE 1 AC3 6 ASP A 421 ARG A 422 SER A 425 ALA A 426 SITE 2 AC3 6 GLY A 621 HOH A1102 SITE 1 AC4 18 PRO A 469 ASP A 470 ASN A 472 GLN A 475 SITE 2 AC4 18 GLY A 495 THR A 496 GLY A 497 LYS A 498 SITE 3 AC4 18 THR A 499 VAL A 500 TYR A 702 ARG A 703 SITE 4 AC4 18 GLU A 833 HOH A1128 ALF A1005 MG A1006 SITE 5 AC4 18 HOH A1119 HOH A1134 SITE 1 AC5 12 PRO A 494 GLY A 495 LYS A 498 GLU A 637 SITE 2 AC5 12 GLN A 665 ARG A 703 GLY A 831 ARG A 865 SITE 3 AC5 12 HOH A1195 HOH A1104 ADP A1004 MG A1006 SITE 1 AC6 6 THR A 499 HOH A1195 HOH A1106 ADP A1004 SITE 2 AC6 6 ALF A1005 HOH A1119 SITE 1 AC7 6 TYR A 806 MET A 807 PHE A 809 SER A 810 SITE 2 AC7 6 SER A 812 THR A 815 CRYST1 77.066 101.896 112.320 90.00 90.00 90.00 P 21 21 21 4 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 0.012976 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009814 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008903 0.00000