HEADER RNA BINDING PROTEIN 09-FEB-21 7NH2 TITLE CRYSTAL STRUCTURE OF TOXOPLASMA CPSF4-YTH DOMAIN BOUND TO M6A 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 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 KEYWDS YTH, CLEAVAGE AND POLYADENYLATION, RNA, M6A, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.SWALE,M.W.BOWLER REVDAT 3 31-JAN-24 7NH2 1 REMARK REVDAT 2 28-JUL-21 7NH2 1 JRNL REVDAT 1 21-JUL-21 7NH2 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 30007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1532 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 30.7600 - 3.0000 0.98 2723 151 0.1748 0.1893 REMARK 3 2 3.0000 - 2.3800 0.94 2618 152 0.1813 0.1829 REMARK 3 3 2.3800 - 2.0800 0.94 2631 148 0.1618 0.1849 REMARK 3 4 2.0800 - 1.8900 0.93 2584 149 0.1638 0.1745 REMARK 3 5 1.8900 - 1.7500 0.94 2631 131 0.1778 0.1991 REMARK 3 6 1.7500 - 1.6500 0.94 2630 151 0.1776 0.1976 REMARK 3 7 1.6500 - 1.5700 0.92 2607 131 0.1947 0.2316 REMARK 3 8 1.5700 - 1.5000 0.91 2504 135 0.2107 0.2377 REMARK 3 9 1.5000 - 1.4400 0.91 2560 123 0.2174 0.2229 REMARK 3 10 1.4400 - 1.3900 0.90 2531 122 0.2296 0.2279 REMARK 3 11 1.3900 - 1.3500 0.88 2456 139 0.2416 0.2609 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) : 0.139 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.998 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.21 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 : 0.005 1298 REMARK 3 ANGLE : 0.822 1762 REMARK 3 CHIRALITY : 0.077 185 REMARK 3 PLANARITY : 0.004 227 REMARK 3 DIHEDRAL : 15.807 485 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 7NH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9660 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.349 REMARK 200 RESOLUTION RANGE LOW (A) : 30.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 40.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PEG 400, 0.1M SODIUM ACETATE PH REMARK 280 4.5 AND 0.2M LISO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 KCAL/MOL 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 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 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 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 847 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 848 DISTANCE = 6.68 ANGSTROMS 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 PG4 A 601 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OYK A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NG2 RELATED DB: PDB REMARK 900 SAME CONSTRUCT AS 7NG2 BUT BOUND TO M6A DBREF 7NH2 A 434 598 UNP S8F6K2 S8F6K2_TOXGM 434 598 SEQADV 7NH2 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 HET PG4 A 601 11 HET OYK A 602 12 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM OYK ~{N},9-DIMETHYLPURIN-6-AMINE FORMUL 2 PG4 C8 H18 O5 FORMUL 3 OYK C7 H9 N5 FORMUL 4 HOH *148(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 ARG A 505 O MET A 533 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 THR A 565 VAL A 567 -1 O THR A 565 N ILE A 450 SITE 1 AC1 3 LYS A 446 SER A 573 HOH A 758 SITE 1 AC2 14 GLN A 443 ASN A 454 TRP A 468 ALA A 469 SITE 2 AC2 14 THR A 470 TRP A 519 VAL A 522 LEU A 526 SITE 3 AC2 14 ASP A 563 HOH A 710 HOH A 731 HOH A 732 SITE 4 AC2 14 HOH A 740 HOH A 836 CRYST1 32.474 35.221 38.177 114.51 100.44 97.77 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 0.030794 0.004200 0.008475 0.00000 SCALE2 0.000000 0.028655 0.014474 0.00000 SCALE3 0.000000 0.000000 0.029839 0.00000