HEADER RNA BINDING PROTEIN 25-JUL-13 4LUN TITLE STRUCTURE OF THE N-TERMINAL MIF4G DOMAIN FROM S. CEREVISIAE UPF2, A TITLE 2 PROTEIN INVOLVED IN THE DEGRADATION OF MRNAS CONTAINING PREMATURE TITLE 3 STOP CODONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NONSENSE-MEDIATED MRNA DECAY PROTEIN 2; COMPND 3 CHAIN: U; COMPND 4 FRAGMENT: UPF2 DOMAIN, UNP RESIDUES 1-310; COMPND 5 SYNONYM: UP-FRAMESHIFT SUPPRESSOR 2; COMPND 6 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: IFS1, NMD2, SUA1, UPF2, YHR077C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 CODON+; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMG567 KEYWDS HEAT-REPEAT, MRNA DECAY, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.FOURATI,B.ROY,C.MILLAN,P.D.COURREUX,S.KERVESTIN,H.VAN TILBEURGH, AUTHOR 2 F.HE,I.USON,A.JACOBSON,M.GRAILLE REVDAT 4 28-FEB-24 4LUN 1 REMARK REVDAT 3 05-MAY-21 4LUN 1 JRNL REMARK SEQADV REVDAT 2 27-DEC-17 4LUN 1 TITLE REVDAT 1 30-JUL-14 4LUN 0 JRNL AUTH Z.FOURATI,B.ROY,C.MILLAN,P.D.COUREUX,S.KERVESTIN, JRNL AUTH 2 H.VAN TILBEURGH,F.HE,I.USON,A.JACOBSON,M.GRAILLE JRNL TITL A HIGHLY CONSERVED REGION ESSENTIAL FOR NMD IN THE UPF2 JRNL TITL 2 N-TERMINAL DOMAIN. JRNL REF J.MOL.BIOL. V. 426 3689 2014 JRNL REFN ESSN 1089-8638 JRNL PMID 25277656 JRNL DOI 10.1016/J.JMB.2014.09.015 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 36056 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1803 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 41.1964 - 3.8585 0.97 2677 141 0.1692 0.1938 REMARK 3 2 3.8585 - 3.0629 0.98 2659 140 0.1831 0.2235 REMARK 3 3 3.0629 - 2.6758 0.98 2643 140 0.2029 0.2359 REMARK 3 4 2.6758 - 2.4312 0.99 2656 139 0.1918 0.2501 REMARK 3 5 2.4312 - 2.2569 0.99 2645 140 0.1824 0.2087 REMARK 3 6 2.2569 - 2.1239 0.99 2641 139 0.1793 0.2107 REMARK 3 7 2.1239 - 2.0175 0.99 2658 139 0.1890 0.2368 REMARK 3 8 2.0175 - 1.9297 1.00 2663 141 0.1962 0.2429 REMARK 3 9 1.9297 - 1.8554 0.99 2658 139 0.1974 0.2798 REMARK 3 10 1.8554 - 1.7914 1.00 2642 140 0.2194 0.2494 REMARK 3 11 1.7914 - 1.7354 0.99 2617 137 0.2393 0.3490 REMARK 3 12 1.7354 - 1.6858 0.99 2631 139 0.2719 0.3133 REMARK 3 13 1.6858 - 1.6414 0.92 2463 129 0.2862 0.3280 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 33.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.810 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.69150 REMARK 3 B22 (A**2) : 8.81250 REMARK 3 B33 (A**2) : -4.12110 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.22670 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 2622 REMARK 3 ANGLE : 0.993 3530 REMARK 3 CHIRALITY : 0.071 394 REMARK 3 PLANARITY : 0.003 452 REMARK 3 DIHEDRAL : 14.984 1003 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 4LUN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36059 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.62600 REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL PH 8.5 AND 30% PEG 400, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K. 100MM NACL, 100 REMARK 280 MM BICINE PH9 AND 30% PEG MME 550, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 25.46350 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: U 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 LEU U 25 REMARK 465 LYS U 26 REMARK 465 SER U 27 REMARK 465 LYS U 28 REMARK 465 HIS U 316 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 ASN U 105 -138.80 50.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL U 401 DBREF 4LUN U 1 310 UNP P38798 NMD2_YEAST 1 310 SEQADV 4LUN HIS U 311 UNP P38798 EXPRESSION TAG SEQADV 4LUN HIS U 312 UNP P38798 EXPRESSION TAG SEQADV 4LUN HIS U 313 UNP P38798 EXPRESSION TAG SEQADV 4LUN HIS U 314 UNP P38798 EXPRESSION TAG SEQADV 4LUN HIS U 315 UNP P38798 EXPRESSION TAG SEQADV 4LUN HIS U 316 UNP P38798 EXPRESSION TAG SEQRES 1 U 316 MET ASP ASP GLY ARG LYS LYS GLU LEU HIS ASP LEU ASN SEQRES 2 U 316 THR ARG ALA TRP ASN GLY GLU GLU VAL PHE PRO LEU LYS SEQRES 3 U 316 SER LYS LYS LEU ASP SER SER ILE LYS ARG ASN THR GLY SEQRES 4 U 316 PHE ILE LYS LYS LEU LYS LYS GLY PHE VAL LYS GLY SER SEQRES 5 U 316 GLU SER SER LEU LEU LYS ASP LEU SER GLU ALA SER LEU SEQRES 6 U 316 GLU LYS TYR LEU SER GLU ILE ILE VAL THR VAL THR GLU SEQRES 7 U 316 CYS LEU LEU ASN VAL LEU ASN LYS ASN ASP ASP VAL ILE SEQRES 8 U 316 ALA ALA VAL GLU ILE ILE SER GLY LEU HIS GLN ARG PHE SEQRES 9 U 316 ASN GLY ARG PHE THR SER PRO LEU LEU GLY ALA PHE LEU SEQRES 10 U 316 GLN ALA PHE GLU ASN PRO SER VAL ASP ILE GLU SER GLU SEQRES 11 U 316 ARG ASP GLU LEU GLN ARG ILE THR ARG VAL LYS GLY ASN SEQRES 12 U 316 LEU ARG VAL PHE THR GLU LEU TYR LEU VAL GLY VAL PHE SEQRES 13 U 316 ARG THR LEU ASP ASP ILE GLU SER LYS ASP ALA ILE PRO SEQRES 14 U 316 ASN PHE LEU GLN LYS LYS THR GLY ARG LYS ASP PRO LEU SEQRES 15 U 316 LEU PHE SER ILE LEU ARG GLU ILE LEU ASN TYR LYS PHE SEQRES 16 U 316 LYS LEU GLY PHE THR THR THR ILE ALA THR ALA PHE ILE SEQRES 17 U 316 LYS LYS PHE ALA PRO LEU PHE ARG ASP ASP ASP ASN SER SEQRES 18 U 316 TRP ASP ASP LEU ILE TYR ASP SER LYS LEU LYS GLY ALA SEQRES 19 U 316 LEU GLN SER LEU PHE LYS ASN PHE ILE ASP ALA THR PHE SEQRES 20 U 316 ALA ARG ALA THR GLU LEU HIS LYS LYS VAL ASN LYS LEU SEQRES 21 U 316 GLN ARG GLU HIS GLN LYS CYS GLN ILE ARG THR GLY LYS SEQRES 22 U 316 LEU ARG ASP GLU TYR VAL GLU GLU TYR ASP LYS LEU LEU SEQRES 23 U 316 PRO ILE PHE ILE ARG PHE LYS THR SER ALA ILE THR LEU SEQRES 24 U 316 GLY GLU PHE PHE LYS LEU GLU ILE PRO GLU LEU HIS HIS SEQRES 25 U 316 HIS HIS HIS HIS HET CL U 401 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *165(H2 O) HELIX 1 1 ASP U 2 ASN U 18 1 17 HELIX 2 2 SER U 33 LYS U 45 1 13 HELIX 3 3 GLY U 51 SER U 61 1 11 HELIX 4 4 LEU U 65 LYS U 67 5 3 HELIX 5 5 TYR U 68 ASN U 82 1 15 HELIX 6 6 LYS U 86 ASN U 105 1 20 HELIX 7 7 ASN U 105 LEU U 117 1 13 HELIX 8 8 GLN U 118 GLU U 121 5 4 HELIX 9 9 SER U 129 VAL U 153 1 25 HELIX 10 10 THR U 158 ILE U 162 5 5 HELIX 11 11 PRO U 169 GLN U 173 5 5 HELIX 12 12 PRO U 181 LEU U 191 1 11 HELIX 13 13 ASN U 192 TYR U 193 5 2 HELIX 14 14 LYS U 194 PHE U 199 5 6 HELIX 15 15 THR U 200 PHE U 211 1 12 HELIX 16 16 ALA U 212 PHE U 215 5 4 HELIX 17 17 TRP U 222 ILE U 226 5 5 HELIX 18 18 LYS U 230 GLY U 272 1 43 HELIX 19 19 ASP U 276 LYS U 304 1 29 SITE 1 AC1 4 TYR U 151 PRO U 181 ASP U 228 HOH U 505 CRYST1 41.813 50.927 71.993 90.00 99.96 90.00 P 1 21 1 2 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 0.023916 0.000000 0.004198 0.00000 SCALE2 0.000000 0.019636 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014103 0.00000