HEADER SIGNALING PROTEIN 02-JUL-24 9CI7 TITLE STRUCTURE OF PNUTS:TOX4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT COMPND 3 10; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: MHC CLASS I REGION PROLINE-RICH PROTEIN CAT53,PHOSPHATASE 1 COMPND 6 NUCLEAR TARGETING SUBUNIT,PROTEIN PNUTS; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TOX HIGH MOBILITY GROUP BOX FAMILY MEMBER 4; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: EPIDERMAL LANGERHANS CELL PROTEIN LCP1; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PPP1R10, CAT53, PNUTS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: TOX4, C14ORF92, KIAA0737; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PNUTS, PPP1R10, TRANSCRIPTIONAL ELONGATION FACTOR S-II HOMOLOGY N- KEYWDS 2 TERMINAL DOMAIN. TOX4, ZINC BINDING PROTEIN, COMPLEX, SIGNALING KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.PAGE,W.PETI,X.WANG REVDAT 1 21-MAY-25 9CI7 0 JRNL AUTH L.DUNCALF,X.WANG,A.A.ALJABRI,A.E.CAMPBELL,R.Q.ALHARBI, JRNL AUTH 2 I.DONALDSON,A.HAYES,W.PETI,R.PAGE,D.BENNETT JRNL TITL PNUTS:PP1 RECRUITMENT TO TOX4 REGULATES CHROMOSOMAL JRNL TITL 2 DISPERSAL IN DROSOPHILA GERMLINE DEVELOPMENT. JRNL REF CELL REP V. 44 15693 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 40347473 JRNL DOI 10.1016/J.CELREP.2025.115693 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 35.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 15916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 783 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 35.3200 - 3.8100 0.98 2537 133 0.1455 0.1555 REMARK 3 2 3.8100 - 3.0300 1.00 2569 107 0.1987 0.2269 REMARK 3 3 3.0300 - 2.6400 0.99 2512 140 0.2216 0.2703 REMARK 3 4 2.6400 - 2.4000 1.00 2517 142 0.2413 0.2749 REMARK 3 5 2.4000 - 2.2300 0.99 2539 121 0.2041 0.2261 REMARK 3 6 2.2300 - 2.1000 0.97 2459 140 0.2476 0.2888 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.814 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.32 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 : 0.001 1629 REMARK 3 ANGLE : 0.336 2204 REMARK 3 CHIRALITY : 0.033 258 REMARK 3 PLANARITY : 0.003 276 REMARK 3 DIHEDRAL : 10.089 619 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 9CI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAY-17 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.192 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, AIMLESS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 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) : 0.49800 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: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.5, 1 M LICL, 15% REMARK 280 PEG6K, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.38833 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.77667 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 48.58250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 80.97083 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.19417 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: 2970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 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 SER A 148 REMARK 465 SER A 149 REMARK 465 THR A 150 REMARK 465 GLN A 151 REMARK 465 PRO A 152 REMARK 465 ALA A 153 REMARK 465 GLU A 154 REMARK 465 LYS A 155 REMARK 465 ASP A 156 REMARK 465 LYS A 157 REMARK 465 LYS A 158 REMARK 465 LYS A 159 REMARK 465 ARG A 160 REMARK 465 LYS B 621 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 B 613 -169.11 -103.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 3 NE2 REMARK 620 2 HIS A 100 ND1 76.7 REMARK 620 3 HIS B 569 NE2 115.7 81.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 572 SG REMARK 620 2 CYS B 577 SG 111.1 REMARK 620 3 CYS B 592 SG 116.9 104.4 REMARK 620 4 CYS B 596 SG 108.6 115.0 100.7 REMARK 620 N 1 2 3 DBREF 9CI7 A 5 160 UNP O55000 PP1RA_RAT 5 160 DBREF 9CI7 B 571 621 UNP O94842 TOX4_HUMAN 571 621 SEQADV 9CI7 GLY A 2 UNP O55000 EXPRESSION TAG SEQADV 9CI7 HIS A 3 UNP O55000 EXPRESSION TAG SEQADV 9CI7 MET A 4 UNP O55000 EXPRESSION TAG SEQADV 9CI7 SER A 48 UNP O55000 CYS 48 ENGINEERED MUTATION SEQADV 9CI7 GLY B 568 UNP O94842 EXPRESSION TAG SEQADV 9CI7 HIS B 569 UNP O94842 EXPRESSION TAG SEQADV 9CI7 MET B 570 UNP O94842 EXPRESSION TAG SEQADV 9CI7 SER B 601 UNP O94842 CYS 601 ENGINEERED MUTATION SEQRES 1 A 159 GLY HIS MET PRO ILE ASP PRO LYS GLU LEU LEU LYS GLY SEQRES 2 A 159 LEU ASP SER PHE LEU THR ARG ASP GLY GLU VAL LYS SER SEQRES 3 A 159 VAL ASP GLY ILE ALA LYS ILE PHE SER LEU MET LYS GLU SEQRES 4 A 159 ALA ARG LYS MET VAL SER ARG SER THR TYR LEU ASN ILE SEQRES 5 A 159 ILE LEU GLN THR ARG ALA PRO GLU VAL LEU VAL LYS PHE SEQRES 6 A 159 ILE ASP VAL GLY GLY TYR LYS LEU LEU ASN SER TRP LEU SEQRES 7 A 159 THR TYR SER LYS THR THR ASN ASN ILE PRO LEU LEU GLN SEQRES 8 A 159 GLN ILE LEU LEU THR LEU GLN HIS LEU PRO LEU THR VAL SEQRES 9 A 159 ASP HIS LEU LYS GLN ASN ASN THR ALA LYS LEU VAL LYS SEQRES 10 A 159 GLN LEU SER LYS SER SER GLU ASP GLU GLU LEU ARG LYS SEQRES 11 A 159 LEU ALA SER VAL LEU VAL SER ASP TRP MET ALA VAL ILE SEQRES 12 A 159 ARG SER GLN SER SER THR GLN PRO ALA GLU LYS ASP LYS SEQRES 13 A 159 LYS LYS ARG SEQRES 1 B 54 GLY HIS MET ARG CYS VAL ARG SER GLY CYS GLU ASN PRO SEQRES 2 B 54 PRO ILE VAL SER LYS ASP TRP ASP ASN GLU TYR CYS SER SEQRES 3 B 54 ASN GLU CYS VAL VAL LYS HIS SER ARG ASP VAL PHE LEU SEQRES 4 B 54 ALA TRP VAL ALA SER ARG ASN SER ASN THR VAL VAL PHE SEQRES 5 B 54 VAL LYS HET CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET ZN A 204 1 HET NA A 205 1 HET ZN B 701 1 HET CL B 702 1 HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM NA SODIUM ION FORMUL 3 CL 4(CL 1-) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 NA NA 1+ FORMUL 10 HOH *128(H2 O) HELIX 1 AA1 ASP A 7 LEU A 15 1 9 HELIX 2 AA2 SER A 27 GLU A 40 1 14 HELIX 3 AA3 LYS A 43 THR A 57 1 15 HELIX 4 AA4 ALA A 59 VAL A 69 1 11 HELIX 5 AA5 GLY A 70 THR A 85 1 16 HELIX 6 AA6 ASN A 87 LEU A 101 1 15 HELIX 7 AA7 THR A 104 LYS A 109 1 6 HELIX 8 AA8 ASN A 112 SER A 124 1 13 HELIX 9 AA9 ASP A 126 SER A 146 1 21 HELIX 10 AB1 SER B 593 ARG B 612 1 20 LINK NE2 HIS A 3 ZN ZN A 204 1555 1555 2.03 LINK ND1 HIS A 100 ZN ZN A 204 1555 6655 2.28 LINK ZN ZN A 204 NE2 HIS B 569 1555 1555 2.02 LINK SG CYS B 572 ZN ZN B 701 1555 1555 2.35 LINK SG CYS B 577 ZN ZN B 701 1555 1555 2.30 LINK SG CYS B 592 ZN ZN B 701 1555 1555 2.32 LINK SG CYS B 596 ZN ZN B 701 1555 1555 2.33 CRYST1 70.630 70.630 97.165 90.00 90.00 120.00 P 61 6 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 0.014158 0.008174 0.000000 0.00000 SCALE2 0.000000 0.016349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010292 0.00000 CONECT 14 1606 CONECT 1186 1606 CONECT 1211 1608 CONECT 1245 1608 CONECT 1371 1608 CONECT 1400 1608 CONECT 1606 14 1186 CONECT 1608 1211 1245 1371 1400 MASTER 265 0 7 10 0 0 0 6 1716 2 8 18 END