HEADER RNA BINDING PROTEIN 16-FEB-21 7NJC TITLE CRYSTAL STRUCTURE OF THE TOXOPLASMA CPSF4 YTH-DOMAIN IN COMPLEX WITH A TITLE 2 7 MER M6A-MODIFIED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER (CCCH TYPE) MOTIF-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CPSF4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*(6MZ)P*CP*A)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: MODIFIED N6-ADENOSINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII (STRAIN ATCC 50611 / ME49); SOURCE 3 ORGANISM_TAXID: 508771; SOURCE 4 STRAIN: ATCC 50611 / ME49; SOURCE 5 GENE: TGME49_201200; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-RIL; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: BL21-RIL; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS YTH, CLEAVAGE AND POLYADENYLATION, RNA, M6A, RNA RECOGNITION PROTEIN, KEYWDS 2 RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SWALE,M.W.BOWLER REVDAT 3 31-JAN-24 7NJC 1 REMARK REVDAT 2 28-JUL-21 7NJC 1 JRNL REVDAT 1 21-JUL-21 7NJC 0 JRNL AUTH D.C.FARHAT,M.W.BOWLER,G.COMMUNIE,D.PONTIER,L.BELMUDES,C.MAS, JRNL AUTH 2 C.CORRAO,Y.COUTE,A.BOUGDOUR,T.LAGRANGE,M.A.HAKIMI,C.SWALE JRNL TITL A PLANT-LIKE MECHANISM COUPLING M6A READING TO JRNL TITL 2 POLYADENYLATION SAFEGUARDS TRANSCRIPTOME INTEGRITY AND JRNL TITL 3 DEVELOPMENTAL GENE PARTITIONING IN TOXOPLASMA . JRNL REF ELIFE V. 10 2021 JRNL REFN ESSN 2050-084X JRNL PMID 34263725 JRNL DOI 10.7554/ELIFE.68312 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.130 REMARK 3 COMPLETENESS FOR RANGE (%) : 62.9 REMARK 3 NUMBER OF REFLECTIONS : 19180 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1918 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 31.0400 - 3.3200 0.98 1921 213 0.1588 0.1764 REMARK 3 2 3.3100 - 2.6300 0.97 1898 212 0.1628 0.1796 REMARK 3 3 2.6300 - 2.3000 0.97 1901 211 0.1575 0.1730 REMARK 3 4 2.3000 - 2.0900 0.97 1913 212 0.1354 0.1607 REMARK 3 5 2.0900 - 1.9400 0.97 1893 211 0.1254 0.1556 REMARK 3 6 1.9400 - 1.8300 0.96 1875 208 0.1167 0.1494 REMARK 3 7 1.8200 - 1.7300 0.95 1868 208 0.1161 0.1671 REMARK 3 8 1.7300 - 1.6600 0.69 1337 148 0.1105 0.1609 REMARK 3 9 1.6600 - 1.5900 0.47 919 102 0.1135 0.1696 REMARK 3 10 1.5900 - 1.5400 0.35 675 75 0.1029 0.1385 REMARK 3 11 1.5400 - 1.4900 0.24 482 54 0.1127 0.1617 REMARK 3 12 1.4900 - 1.4500 0.17 333 37 0.1038 0.1448 REMARK 3 13 1.4500 - 1.4100 0.09 171 19 0.1620 0.1883 REMARK 3 14 1.4100 - 1.3800 0.04 76 8 0.1622 0.1898 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) : 0.099 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.276 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.72 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 : 0.006 1302 REMARK 3 ANGLE : 0.915 1769 REMARK 3 CHIRALITY : 0.440 190 REMARK 3 PLANARITY : 0.005 217 REMARK 3 DIHEDRAL : 12.625 486 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 7NJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292114003. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 31.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 62.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 6.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 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: 4R3I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE PH: 4.6 IN 40% PEG REMARK 280 200, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 1410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A 433 REMARK 465 ASP A 434 REMARK 465 PRO A 435 REMARK 465 PHE A 436 REMARK 465 GLY A 437 REMARK 465 HIS A 438 REMARK 465 VAL A 439 REMARK 465 ALA A 440 REMARK 465 SER A 441 REMARK 465 THR A 591 REMARK 465 GLY A 592 REMARK 465 ILE A 593 REMARK 465 ASP A 594 REMARK 465 PRO A 595 REMARK 465 ALA A 596 REMARK 465 THR A 597 REMARK 465 ARG A 598 REMARK 465 G B -1 REMARK 465 A B 0 REMARK 465 6MZ B 1 REMARK 465 U B 4 REMARK 465 U B 5 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 PHE A 515 53.88 39.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 761 DISTANCE = 6.24 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NG2 RELATED DB: PDB REMARK 900 TOXOPLASMA CPSF4 IN APO FORM REMARK 900 RELATED ID: 7NH2 RELATED DB: PDB REMARK 900 TOXOPLASMA CPSF4 BOUND TO M6A DBREF 7NJC A 434 598 UNP S8F6K2 S8F6K2_TOXGM 434 598 DBREF 7NJC B -1 5 PDB 7NJC 7NJC -1 5 SEQADV 7NJC GLY A 433 UNP S8F6K2 EXPRESSION TAG SEQRES 1 A 166 GLY ASP PRO PHE GLY HIS VAL ALA SER PRO GLN SER THR SEQRES 2 A 166 LYS ARG PHE PHE ILE ILE LYS SER ASN ARG MET SER ASN SEQRES 3 A 166 ILE TYR THR SER ILE GLN HIS GLY VAL TRP ALA THR SER SEQRES 4 A 166 LYS GLY ASN SER ARG LYS LEU SER ASN ALA PHE THR SER SEQRES 5 A 166 THR ASP HIS VAL LEU LEU LEU PHE SER ALA ASN GLU SER SEQRES 6 A 166 GLY GLY PHE GLN GLY PHE GLY ARG MET MET SER LEU PRO SEQRES 7 A 166 ASP PRO GLN LEU PHE PRO GLY ILE TRP GLY PRO VAL GLN SEQRES 8 A 166 LEU ARG LEU GLY SER ASN PHE ARG VAL MET TRP LEU LYS SEQRES 9 A 166 GLN CYS LYS ILE GLU PHE GLU GLU LEU GLY LYS VAL THR SEQRES 10 A 166 ASN PRO TRP ASN ASP ASP LEU PRO LEU ARG LYS SER ARG SEQRES 11 A 166 ASP GLY THR GLU VAL PRO PRO ALA LEU GLY SER LEU LEU SEQRES 12 A 166 CYS THR TRP MET SER GLN ARG PRO SER GLU ASP LEU LEU SEQRES 13 A 166 ALA GLY THR GLY ILE ASP PRO ALA THR ARG SEQRES 1 B 7 G A 6MZ C A U U HET TOE A 600 11 HET 6MD B 101 20 HETNAM TOE 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL HETNAM 6MD N-METHYLADENOSINE FORMUL 3 TOE C7 H16 O4 FORMUL 4 6MD C11 H15 N5 O4 FORMUL 5 HOH *61(H2 O) HELIX 1 AA1 ARG A 455 GLY A 466 1 12 HELIX 2 AA2 SER A 471 SER A 484 1 14 HELIX 3 AA3 GLY A 520 LEU A 526 5 7 HELIX 4 AA4 GLU A 543 GLY A 546 5 4 HELIX 5 AA5 PRO A 557 SER A 561 5 5 HELIX 6 AA6 PRO A 568 GLN A 581 1 14 SHEET 1 AA1 6 VAL A 467 TRP A 468 0 SHEET 2 AA1 6 PHE A 530 GLU A 541 -1 O PHE A 530 N TRP A 468 SHEET 3 AA1 6 GLY A 499 MET A 506 -1 N PHE A 503 O LEU A 535 SHEET 4 AA1 6 THR A 485 ALA A 494 -1 N LEU A 490 O GLY A 504 SHEET 5 AA1 6 SER A 444 SER A 453 1 N ARG A 447 O LEU A 489 SHEET 6 AA1 6 GLU A 566 VAL A 567 -1 O VAL A 567 N PHE A 448 LINK P C B 2 O3' 6MD B 101 1555 1555 1.55 CRYST1 32.442 35.153 38.350 114.68 100.70 97.65 P 1 1 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 0.030824 0.004142 0.008650 0.00000 SCALE2 0.000000 0.028703 0.014631 0.00000 SCALE3 0.000000 0.000000 0.029786 0.00000