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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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