HEADER SIGNALING PROTEIN 08-JUL-20 7CIO TITLE MOLECULAR INTERACTIONS OF CYTOPLASMIC REGION OF CTLA-4 WITH SH2 TITLE 2 DOMAINS OF PI3-KINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PTDINS-3-KINASE REGULATORY SUBUNIT ALPHA, COMPND 5 PHOSPHATIDYLINOSITOL 3-KINASE 85 KDA REGULATORY SUBUNIT ALPHA,PTDINS- COMPND 6 3-KINASE REGULATORY SUBUNIT P85-ALPHA; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4,CTLA-4; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PIK3R1, GRB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-2; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS T-CELL, CD28, PHOSPHOPEPTIDES, PROTEIN ENGINEERING, THERMOSTABILITY, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.IIYAMA,N.NUMOTO,S.OGAWA,M.KURODA,H.MORII,R.ABE,N.ITO,M.ODA REVDAT 4 30-OCT-24 7CIO 1 REMARK REVDAT 3 29-NOV-23 7CIO 1 REMARK REVDAT 2 17-MAR-21 7CIO 1 JRNL REVDAT 1 09-DEC-20 7CIO 0 JRNL AUTH M.IIYAMA,N.NUMOTO,S.OGAWA,M.KURODA,H.MORII,R.ABE,N.ITO,M.ODA JRNL TITL MOLECULAR INTERACTIONS OF THE CTLA-4 CYTOPLASMIC REGION WITH JRNL TITL 2 THE PHOSPHOINOSITIDE 3-KINASE SH2 DOMAINS. JRNL REF MOL.IMMUNOL. V. 131 51 2021 JRNL REFN ISSN 0161-5890 JRNL PMID 33386150 JRNL DOI 10.1016/J.MOLIMM.2020.12.002 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 40725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2037 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 34.1000 - 2.7100 1.00 2866 151 0.1510 0.1570 REMARK 3 2 2.7100 - 2.1500 1.00 2732 139 0.1543 0.1871 REMARK 3 3 2.1500 - 1.8800 1.00 2731 122 0.1367 0.1583 REMARK 3 4 1.8800 - 1.7100 1.00 2676 156 0.1393 0.1722 REMARK 3 5 1.7100 - 1.5900 1.00 2674 141 0.1224 0.1797 REMARK 3 6 1.5900 - 1.4900 1.00 2646 145 0.1298 0.1687 REMARK 3 7 1.4900 - 1.4200 1.00 2692 128 0.1495 0.1645 REMARK 3 8 1.4200 - 1.3600 1.00 2664 135 0.1636 0.1735 REMARK 3 9 1.3600 - 1.3000 1.00 2645 142 0.1810 0.2290 REMARK 3 10 1.3000 - 1.2600 1.00 2636 161 0.1926 0.2308 REMARK 3 11 1.2600 - 1.2200 1.00 2630 150 0.1983 0.2412 REMARK 3 12 1.2200 - 1.1800 1.00 2651 126 0.1954 0.2618 REMARK 3 13 1.1800 - 1.1500 0.98 2568 140 0.2020 0.2186 REMARK 3 14 1.1500 - 1.1300 0.81 2128 114 0.2227 0.2537 REMARK 3 15 1.1300 - 1.1000 0.66 1749 87 0.2400 0.2568 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) : 0.113 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.885 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.78 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 : 0.012 984 REMARK 3 ANGLE : 1.312 1346 REMARK 3 CHIRALITY : 0.108 148 REMARK 3 PLANARITY : 0.010 173 REMARK 3 DIHEDRAL : 11.832 365 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 7CIO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1300017685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40740 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.88400 REMARK 200 FOR SHELL : 1.800 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: 5AUL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE PH 4.6, 30% PEG 4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 20.61050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.81400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.78150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.81400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.61050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.78150 REMARK 290 SMTRY3 4 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: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 PRO A 684 37.35 -95.71 REMARK 500 LEU A 710 50.11 -117.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CIO A 614 720 UNP P27986 P85A_HUMAN 614 720 DBREF 7CIO B 189 196 UNP P16410 CTLA4_HUMAN 199 206 SEQADV 7CIO GLY A 612 UNP P27986 EXPRESSION TAG SEQADV 7CIO SER A 613 UNP P27986 EXPRESSION TAG SEQADV 7CIO SER A 656 UNP P27986 CYS 656 ENGINEERED MUTATION SEQADV 7CIO VAL A 659 UNP P27986 CYS 659 ENGINEERED MUTATION SEQADV 7CIO LEU A 670 UNP P27986 CYS 670 ENGINEERED MUTATION SEQRES 1 A 109 GLY SER GLU ASP LEU PRO HIS HIS ASP GLU LYS THR TRP SEQRES 2 A 109 ASN VAL GLY SER SER ASN ARG ASN LYS ALA GLU ASN LEU SEQRES 3 A 109 LEU ARG GLY LYS ARG ASP GLY THR PHE LEU VAL ARG GLU SEQRES 4 A 109 SER SER LYS GLN GLY SER TYR ALA VAL SER VAL VAL VAL SEQRES 5 A 109 ASP GLY GLU VAL LYS HIS LEU VAL ILE ASN LYS THR ALA SEQRES 6 A 109 THR GLY TYR GLY PHE ALA GLU PRO TYR ASN LEU TYR SER SEQRES 7 A 109 SER LEU LYS GLU LEU VAL LEU HIS TYR GLN HIS THR SER SEQRES 8 A 109 LEU VAL GLN HIS ASN ASP SER LEU ASN VAL THR LEU ALA SEQRES 9 A 109 TYR PRO VAL TYR ALA SEQRES 1 B 8 GLY VAL PTR VAL LYS MET PRO PRO MODRES 7CIO PTR B 191 TYR MODIFIED RESIDUE HET PTR B 191 16 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 HOH *169(H2 O) HELIX 1 AA1 GLY A 612 TRP A 624 5 13 HELIX 2 AA2 ASN A 630 ARG A 639 1 10 HELIX 3 AA3 SER A 690 HIS A 700 1 11 HELIX 4 AA4 SER A 702 HIS A 706 5 5 SHEET 1 AA1 5 GLY A 678 GLY A 680 0 SHEET 2 AA1 5 GLU A 666 THR A 675 -1 N ASN A 673 O GLY A 680 SHEET 3 AA1 5 TYR A 657 VAL A 663 -1 N VAL A 663 O GLU A 666 SHEET 4 AA1 5 THR A 645 GLU A 650 -1 N ARG A 649 O ALA A 658 SHEET 5 AA1 5 TYR A 716 PRO A 717 1 O TYR A 716 N PHE A 646 LINK C VAL B 190 N PTR B 191 1555 1555 1.33 LINK C PTR B 191 N VAL B 192 1555 1555 1.31 CISPEP 1 GLU A 683 PRO A 684 0 0.30 CRYST1 41.221 41.563 59.628 90.00 90.00 90.00 P 21 21 21 4 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 0.024259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016771 0.00000