HEADER PROTEIN BINDING 15-JAN-10 2KT1 TITLE SOLUTION NMR STRUCTURE OF THE SH3 DOMAIN FROM THE P85BETA SUBUNIT OF TITLE 2 PHOSPHATIDYLINOSITOL 3-KINASE FROM H.SAPIENS, NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET HR5531E COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3-KINASE REGULATORY SUBUNIT BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: PI3-KINASE P85 SUBUNIT BETA, PTDINS-3-KINASE P85-BETA; COMPND 6 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: PIK3R2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) + MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: HR5531E-1-80-21.1 KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 TARGET HR5531E, PSI-2, PROTEIN STRUCTURE INITIATIVE, P85BETA SUBUNIT KEYWDS 3 OF PI3K, SH3 DOMAIN, PHOSPHOPROTEIN, POLYMORPHISM, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,L.MA,C.SCHAUDER,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 08-MAY-24 2KT1 1 REMARK REVDAT 4 14-JUN-23 2KT1 1 DBREF REVDAT 3 26-FEB-20 2KT1 1 REMARK SEQADV REVDAT 2 02-FEB-10 2KT1 1 JRNL REVDAT 1 26-JAN-10 2KT1 0 JRNL AUTH J.M.ARAMINI,L.MA,C.SCHAUDER,J.K.EVERETT,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE SH3 DOMAIN FROM THE P85BETA JRNL TITL 2 SUBUNIT OF PHOSPHATIDYLINOSITOL 3-KINASE FROM H.SAPIENS, JRNL TITL 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR5531E JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 972 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS AND 108 DIHEDRAL ANGLE CONSTRAINTS (13.5 CONSTRAINTS REMARK 3 PER RESIDUE, 5.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED REMARK 3 FOR RESIDUES 1 TO 82 BY PSVS 1.4). STRUCTURE DETERMINATION WAS REMARK 3 PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF REMARK 3 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY REMARK 3 RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT REMARK 3 WATER (CNS) WITH PARAM19. REMARK 4 REMARK 4 2KT1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000101537. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.62 MM [U-100% 13C; U-100% 15N] REMARK 210 HR5531E, 20 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 50 UM REMARK 210 DSS, 10 MM DTT, 95% H2O/5% D2O; REMARK 210 0.50 MM [U-5% 13C; U-100% 15N] REMARK 210 HR5531E, 20 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 50 UM REMARK 210 DSS, 10 MM DTT, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-13C AROM NOESY; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HBHANH; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 1D 1H-15N REMARK 210 T1 AND T2; 2D 1H-13C HSQC HIGH REMARK 210 RES. (L/V METHYL REMARK 210 STEREOASSIGNMENT); 2D 1H-15N REMARK 210 HETNOE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, AUTOSTRUCTURE 2.2.1, REMARK 210 PINE 1.0, NMRPIPE 2.3, SPARKY REMARK 210 3.112, TOPSPIN 2.1, PSVS 1.4, REMARK 210 TALOS PLUS, PDBSTAT 5.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE PROTEIN IS PREDOMINANTLY MONOMERIC AT 308 K BY 15N REMARK 210 T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE REMARK 210 RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN REMARK 210 ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. REMARK 210 ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. REMARK 210 BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS REMARK 210 WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL REMARK 210 ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSPLUS. COMPLETENESS OF REMARK 210 NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 94.5%, REMARK 210 SIDE CHAIN, 89.5%, AROMATICS, 86.8%, STEREOSPECIFIC METHYL, 100%, REMARK 210 STEREOSPECIFIC SIDE CHAIN NH2: 80.0%. FINAL STRUCTURE QUALITY REMARK 210 FACTORS (FOR RESIDUE NUMBERS 1 TO 82, PSVS 1.4), WHERE ORDERED REMARK 210 RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 7-16,18-81: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 0.7, HEAVY ATOM, 1.3. (B) RAMACHANDRAN REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.8%, REMARK 210 ADDITIONALLY ALLOWED, 8.1%, GENEROUSLY ALLOWED, 0.1%, DISALLOWED, REMARK 210 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI- REMARK 210 PSI, -0.44/-1.42, ALL, -0.32/-1.89. (D) MOLPROBITY CLASH SCORE REMARK 210 (RAW/Z-): 17.41/-1.46 (E) RPF SCORES FOR GOODNESS OF FIT TO REMARK 210 NOESY DATA (RESIDUES 1-82): RECALL, 0.969, PRECISION, 0.904, F- REMARK 210 MEASURE, 0.935, DP-SCORE, 0.797. (F) NUMBER OF CLOSE CONTACTS REMARK 210 PER 20 MODELS: 7. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN REMARK 210 (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND REMARK 210 HAVE BEEN OMITTED FROM THIS DEPOSITION. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 REMARK 465 HIS A 88 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 1 ARG A 65 17.82 59.64 REMARK 500 2 PRO A 4 47.64 -74.94 REMARK 500 2 CYS A 50 91.70 -161.01 REMARK 500 2 LEU A 78 -65.90 -98.66 REMARK 500 3 PRO A 20 5.42 -66.83 REMARK 500 4 ALA A 2 -68.92 -136.52 REMARK 500 4 PRO A 4 40.69 -100.92 REMARK 500 5 PRO A 4 39.54 -75.17 REMARK 500 5 ASP A 22 -158.43 -81.52 REMARK 500 7 PRO A 4 23.69 -76.47 REMARK 500 7 PRO A 20 -1.41 -59.07 REMARK 500 8 PRO A 4 77.32 -68.59 REMARK 500 8 PRO A 20 -9.29 -56.67 REMARK 500 9 ALA A 2 -158.19 -83.14 REMARK 500 9 PRO A 4 16.01 -67.96 REMARK 500 9 PRO A 20 6.58 -62.09 REMARK 500 9 LEU A 78 -68.11 -100.03 REMARK 500 10 PRO A 71 95.15 -66.29 REMARK 500 11 ALA A 2 -71.11 -61.00 REMARK 500 11 PRO A 27 106.31 -57.91 REMARK 500 12 PRO A 4 24.96 -71.05 REMARK 500 12 ASP A 22 -154.41 -92.55 REMARK 500 12 GLU A 24 105.90 -57.62 REMARK 500 12 GLU A 45 104.76 -56.99 REMARK 500 12 LEU A 78 -61.57 -90.55 REMARK 500 13 PRO A 4 105.82 -37.80 REMARK 500 13 PRO A 20 5.87 -69.54 REMARK 500 14 PRO A 20 5.87 -69.49 REMARK 500 14 LEU A 78 -67.53 -94.66 REMARK 500 15 ASP A 22 -143.62 -78.81 REMARK 500 15 GLU A 45 101.50 -52.93 REMARK 500 17 ALA A 2 -80.56 -98.24 REMARK 500 17 PRO A 20 -5.49 -58.38 REMARK 500 18 ALA A 2 -161.84 -119.05 REMARK 500 18 PRO A 4 86.97 -68.15 REMARK 500 19 PRO A 20 6.85 -67.93 REMARK 500 19 PRO A 71 91.97 -67.17 REMARK 500 20 ARG A 17 140.53 64.32 REMARK 500 20 GLU A 62 0.46 -69.95 REMARK 500 20 ARG A 65 19.44 59.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16681 RELATED DB: BMRB REMARK 900 RELATED ID: HR5531E RELATED DB: TARGETDB DBREF 2KT1 A 1 80 UNP O00459 P85B_HUMAN 1 80 SEQADV 2KT1 LEU A 81 UNP O00459 EXPRESSION TAG SEQADV 2KT1 GLU A 82 UNP O00459 EXPRESSION TAG SEQADV 2KT1 HIS A 83 UNP O00459 EXPRESSION TAG SEQADV 2KT1 HIS A 84 UNP O00459 EXPRESSION TAG SEQADV 2KT1 HIS A 85 UNP O00459 EXPRESSION TAG SEQADV 2KT1 HIS A 86 UNP O00459 EXPRESSION TAG SEQADV 2KT1 HIS A 87 UNP O00459 EXPRESSION TAG SEQADV 2KT1 HIS A 88 UNP O00459 EXPRESSION TAG SEQRES 1 A 88 MET ALA GLY PRO GLU GLY PHE GLN TYR ARG ALA LEU TYR SEQRES 2 A 88 PRO PHE ARG ARG GLU ARG PRO GLU ASP LEU GLU LEU LEU SEQRES 3 A 88 PRO GLY ASP VAL LEU VAL VAL SER ARG ALA ALA LEU GLN SEQRES 4 A 88 ALA LEU GLY VAL ALA GLU GLY GLY GLU ARG CYS PRO GLN SEQRES 5 A 88 SER VAL GLY TRP MET PRO GLY LEU ASN GLU ARG THR ARG SEQRES 6 A 88 GLN ARG GLY ASP PHE PRO GLY THR TYR VAL GLU PHE LEU SEQRES 7 A 88 GLY PRO LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ARG A 35 GLY A 42 1 8 HELIX 2 2 CYS A 50 GLY A 55 1 6 SHEET 1 A 5 ARG A 67 PRO A 71 0 SHEET 2 A 5 TRP A 56 ASN A 61 -1 N GLY A 59 O GLY A 68 SHEET 3 A 5 VAL A 30 SER A 34 -1 N VAL A 32 O LEU A 60 SHEET 4 A 5 GLY A 6 ALA A 11 -1 N TYR A 9 O LEU A 31 SHEET 5 A 5 VAL A 75 LEU A 81 -1 O GLU A 76 N ARG A 10 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1