HEADER PROTEIN BINDING 22-JUL-24 9G7U TITLE STRUCTURE OF THE TESUP-1 PROLINE-RICH BINDING DOMAIN IN COMPLEX WITH TITLE 2 THE PROLINE-RICH REGION OF PIH1D1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LD36051P; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PIH1 DOMAIN CONTAINING 1, ISOFORM D; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CG10057, CG31510-RA, DMEL\CG31510, CG31510, DMEL_CG31510; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 10 ORGANISM_COMMON: FRUIT FLY; SOURCE 11 ORGANISM_TAXID: 7227; SOURCE 12 GENE: PIH1D1, DMEL\CG5792, PIH1D1, CG5792, DMEL_CG5792; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROLINE-RICH BINDING DOMAIN, PROLINE-RICH PEPTIDE, POLYPROLINE II KEYWDS 2 HELIX, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.MANOLOVA,S.FALK REVDAT 1 04-FEB-26 9G7U 0 JRNL AUTH T.MANOLOVA,S.FALK JRNL TITL COTRANSCRIPTIONAL GENE SILENCING BY THE PIWI-PIRNA PATHWAY JRNL TITL 2 DEPENDS ON THE NUCLEAR RNA EXOSOME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 10519 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 521 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 37.5400 - 3.3300 1.00 2619 131 0.2224 0.1994 REMARK 3 2 3.3300 - 2.6500 0.99 2501 124 0.2956 0.3576 REMARK 3 3 2.6500 - 2.3100 0.99 2454 122 0.3005 0.3696 REMARK 3 4 2.3100 - 2.1000 0.99 2424 144 0.2900 0.3575 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.234 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.549 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.16 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 : 0.007 1102 REMARK 3 ANGLE : 0.853 1492 REMARK 3 CHIRALITY : 0.042 149 REMARK 3 PLANARITY : 0.011 194 REMARK 3 DIHEDRAL : 16.732 410 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 702 THROUGH 816) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6513 12.8208 21.8165 REMARK 3 T TENSOR REMARK 3 T11: 0.6024 T22: 0.6137 REMARK 3 T33: 0.4876 T12: 0.1123 REMARK 3 T13: -0.0255 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 1.4539 L22: 0.3376 REMARK 3 L33: 6.5534 L12: -0.9218 REMARK 3 L13: 4.8519 L23: -1.8365 REMARK 3 S TENSOR REMARK 3 S11: 0.2810 S12: 0.4020 S13: -0.0222 REMARK 3 S21: -0.3745 S22: -0.1875 S23: 0.1426 REMARK 3 S31: 0.9251 S32: 0.5854 S33: 0.0187 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 143 THROUGH 153) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1709 18.1232 39.6674 REMARK 3 T TENSOR REMARK 3 T11: 0.6661 T22: 1.1280 REMARK 3 T33: 0.6302 T12: 0.1201 REMARK 3 T13: -0.0799 T23: -0.0345 REMARK 3 L TENSOR REMARK 3 L11: 1.2894 L22: 0.5363 REMARK 3 L33: 1.2826 L12: -0.3877 REMARK 3 L13: 0.2890 L23: -0.1228 REMARK 3 S TENSOR REMARK 3 S11: -0.3062 S12: -0.2551 S13: -0.0873 REMARK 3 S21: 0.9436 S22: 0.3150 S23: 0.8882 REMARK 3 S31: -1.0811 S32: -0.9557 S33: -0.0010 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 9G7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292140523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-23 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 : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87313 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10539 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 62.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M TRIS PH 8.0, 20% W/V PEG 6000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.69350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.54350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.00250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.69350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.54350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.00250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.69350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.54350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.00250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.69350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.54350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.00250 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 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 697 REMARK 465 PRO A 698 REMARK 465 ASP A 699 REMARK 465 SER A 700 REMARK 465 MET A 701 REMARK 465 LEU A 817 REMARK 465 ASP A 818 REMARK 465 LYS A 819 REMARK 465 THR A 820 REMARK 465 ASP B 135 REMARK 465 ASP B 136 REMARK 465 VAL B 137 REMARK 465 GLU B 138 REMARK 465 SER B 139 REMARK 465 ARG B 140 REMARK 465 PRO B 141 REMARK 465 ARG B 142 REMARK 465 SER B 154 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 SER A 702 OG REMARK 470 ASP A 706 CG OD1 OD2 REMARK 470 ASN A 806 CG OD1 ND2 REMARK 470 GLU A 807 CG CD OE1 OE2 REMARK 470 LEU A 808 CG CD1 CD2 REMARK 470 GLU A 809 CG CD OE1 OE2 REMARK 470 GLU A 811 CG CD OE1 OE2 REMARK 470 HIS A 814 CG ND1 CD2 CE1 NE2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9G7L RELATED DB: PDB REMARK 900 9G7L CONTAINS THE SAME FOLDED DOMAIN BUT IN COMPLEX WITH THE REMARK 900 DZFC3H1 PEPTIDE DBREF 9G7U A 702 820 UNP Q9VBX4 Q9VBX4_DROME 702 820 DBREF 9G7U B 135 154 UNP Q9VK58 Q9VK58_DROME 135 154 SEQADV 9G7U GLY A 697 UNP Q9VBX4 EXPRESSION TAG SEQADV 9G7U PRO A 698 UNP Q9VBX4 EXPRESSION TAG SEQADV 9G7U ASP A 699 UNP Q9VBX4 EXPRESSION TAG SEQADV 9G7U SER A 700 UNP Q9VBX4 EXPRESSION TAG SEQADV 9G7U MET A 701 UNP Q9VBX4 EXPRESSION TAG SEQRES 1 A 124 GLY PRO ASP SER MET SER PRO LEU ARG ASP GLY ASP ILE SEQRES 2 A 124 TRP GLN ALA TYR ARG HIS MET VAL ASP LEU LYS VAL ARG SEQRES 3 A 124 GLU LEU ASN VAL SER PHE ASP THR TYR LYS SER ASP PRO SEQRES 4 A 124 GLU GLN HIS PRO SER TYR GLN ALA GLU TRP GLN MET PHE SEQRES 5 A 124 TRP LYS ARG ARG LYS ASP GLU LEU ILE LEU ALA GLY ILE SEQRES 6 A 124 ASN HIS ARG THR TYR ASN PHE GLN ASN GLU TRP ILE ASN SEQRES 7 A 124 PHE PHE ASN ALA ARG ILE GLU GLU LEU TYR SER GLN ASP SEQRES 8 A 124 ILE GLU ASN ILE LYS ILE LYS CYS ARG GLU ARG LEU CYS SEQRES 9 A 124 LEU PRO MET THR ASN ASN GLU LEU GLU ASP GLU LYS TYR SEQRES 10 A 124 HIS VAL HIS LEU ASP LYS THR SEQRES 1 B 20 ASP ASP VAL GLU SER ARG PRO ARG THR PRO SER PRO PRO SEQRES 2 B 20 ARG ASN ILE ASP TRP HIS SER HET GOL A 901 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *10(H2 O) HELIX 1 AA1 ARG A 705 ASP A 734 1 30 HELIX 2 AA2 PRO A 735 HIS A 738 5 4 HELIX 3 AA3 SER A 740 ALA A 759 1 20 HELIX 4 AA4 ASN A 762 TYR A 766 5 5 HELIX 5 AA5 PHE A 768 LEU A 799 1 32 HELIX 6 AA6 ASP A 810 HIS A 814 5 5 CRYST1 41.387 75.087 112.005 90.00 90.00 90.00 I 2 2 2 8 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 0.024162 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013318 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008928 0.00000 CONECT 2065 2066 2067 2071 2072 CONECT 2066 2065 2073 CONECT 2067 2065 2068 2069 2074 CONECT 2068 2067 2075 CONECT 2069 2067 2070 2076 2077 CONECT 2070 2069 2078 CONECT 2071 2065 CONECT 2072 2065 CONECT 2073 2066 CONECT 2074 2067 CONECT 2075 2068 CONECT 2076 2069 CONECT 2077 2069 CONECT 2078 2070 MASTER 281 0 1 6 0 0 0 6 1082 2 14 12 END