HEADER SIGNALING PROTEIN/PROTEIN BINDING 13-AUG-13 2MC1 TITLE SOLUTION STRUCTURE OF THE VAV1 SH2 DOMAIN COMPLEXED WITH A SYK-DERIVED TITLE 2 SINGLY PHOSPHORYLATED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTO-ONCOGENE VAV; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN (UNP RESIDUES 664-767); COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TYROSINE-PROTEIN KINASE SYK; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 338-350; COMPND 10 SYNONYM: SPLEEN TYROSINE KINASE; COMPND 11 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: VAV1, VAV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETTEV411; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: MOUSE; SOURCE 14 ORGANISM_TAXID: 10090 KEYWDS SYK KINASE, TYROSINE KINASE, PHOSPHORYLATED PEPTIDE, PHOSPHOTYROSINE KEYWDS 2 BINDING DOMAIN, B CELL SIGNALING PROTEIN, SIGNALING PROTEIN-PROTEIN KEYWDS 3 BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.CHEN,D.PIRANER,N.M.GORENSTEIN,R.L.GEAHLEN,C.B.POST REVDAT 4 14-JUN-23 2MC1 1 REMARK SEQADV LINK REVDAT 3 02-OCT-13 2MC1 1 JRNL REVDAT 2 04-SEP-13 2MC1 1 JRNL REVDAT 1 28-AUG-13 2MC1 0 JRNL AUTH C.H.CHEN,D.PIRANER,N.M.GORENSTEIN,R.L.GEAHLEN,C.BETH POST JRNL TITL DIFFERENTIAL RECOGNITION OF SYK-BINDING SITES BY EACH OF THE JRNL TITL 2 TWO PHOSPHOTYROSINE-BINDING POCKETS OF THE VAV SH2 DOMAIN. JRNL REF BIOPOLYMERS V. 99 897 2013 JRNL REFN ISSN 0006-3525 JRNL PMID 23955592 JRNL DOI 10.1002/BIP.22371 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MC1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000103458. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 1 MM PEPTIDE, 20 MM REMARK 210 TRIS, 100 MM SODIUM CHLORIDE, 1 REMARK 210 MM DTT, 0.02 % SODIUM AZIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HCCH-TOCSY; 3D H(CCO)NH; 3D C(CO) REMARK 210 NH; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D 1H-13C NOESY AROMATIC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING 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: NULL 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ3 LYS A 719 OG SER B 344 1.18 REMARK 500 HZ1 LYS A 733 OH TYR A 745 1.21 REMARK 500 HZ1 LYS A 716 OG SER A 756 1.22 REMARK 500 O LEU A 685 HZ1 LYS A 710 1.22 REMARK 500 OG1 THR A 730 HZ3 LYS A 755 1.23 REMARK 500 O MET A 676 HE ARG A 696 1.23 REMARK 500 HZ2 LYS A 700 OD2 ASP A 701 1.25 REMARK 500 HZ2 LYS A 755 OD1 ASP B 348 1.26 REMARK 500 O ARG A 688 HZ2 LYS A 710 1.27 REMARK 500 HZ2 LYS A 751 OD1 ASP A 752 1.27 REMARK 500 OE1 GLU A 731 HZ1 LYS A 755 1.28 REMARK 500 O GLY A 680 HG SER A 683 1.28 REMARK 500 O GLY A 725 HH12 ARG A 736 1.28 REMARK 500 HZ3 LYS A 732 OD2 ASP B 348 1.28 REMARK 500 H3 ASP B 338 OE1 GLU B 340 1.30 REMARK 500 HH TYR A 711 O ASP A 758 1.31 REMARK 500 O ALA A 686 HZ3 LYS A 710 1.31 REMARK 500 OE2 GLU A 704 HH TYR B 342 1.31 REMARK 500 HH12 ARG A 688 OXT GLU A 767 1.31 REMARK 500 HH22 ARG A 698 O ASP B 338 1.32 REMARK 500 OE1 GLU A 677 HH12 ARG A 698 1.32 REMARK 500 OE1 GLN A 664 HH TYR A 727 1.32 REMARK 500 HH11 ARG A 678 O VAL B 341 1.33 REMARK 500 O GLU B 343 HG SER B 344 1.33 REMARK 500 HH11 ARG A 728 O LYS A 733 1.33 REMARK 500 HH12 ARG A 678 OE1 GLU B 343 1.33 REMARK 500 OE2 GLU A 724 HH22 ARG A 728 1.34 REMARK 500 O SER A 689 HG1 THR A 692 1.34 REMARK 500 H TYR A 711 O GLU A 714 1.35 REMARK 500 OE1 GLN A 697 H ARG A 698 1.35 REMARK 500 HE1 TRP A 671 OE2 GLU A 743 1.35 REMARK 500 O VAL A 699 H ASP A 701 1.36 REMARK 500 HE ARG A 678 OE2 GLU A 682 1.37 REMARK 500 H2 GLY A 661 OD1 ASP A 665 1.37 REMARK 500 HH22 ARG A 688 O GLU A 767 1.37 REMARK 500 OE2 GLU A 677 H1 ASP B 338 1.38 REMARK 500 O THR A 692 H LYS A 710 1.38 REMARK 500 OE2 GLU A 731 H ASP B 348 1.38 REMARK 500 O PHE A 705 H ILE A 720 1.40 REMARK 500 HH12 ARG A 696 OH TYR B 342 1.40 REMARK 500 O ILE A 709 H LYS A 716 1.42 REMARK 500 H TYR A 727 O PHE A 735 1.43 REMARK 500 O LEU A 694 H SER A 708 1.44 REMARK 500 H ALA A 673 O VAL A 695 1.45 REMARK 500 O GLY A 674 H GLN A 697 1.46 REMARK 500 HE21 GLN A 697 O GLU A 704 1.46 REMARK 500 O GLU A 677 H ALA A 681 1.46 REMARK 500 O GLU A 682 H ALA A 686 1.46 REMARK 500 H LEU A 750 O THR A 759 1.46 REMARK 500 O LEU A 750 H PHE A 754 1.48 REMARK 500 REMARK 500 THIS ENTRY HAS 1309 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL 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 MET A 663 -104.57 -177.57 REMARK 500 1 GLN A 664 42.70 -92.34 REMARK 500 1 SER A 667 -18.22 -48.13 REMARK 500 1 PRO A 675 -8.77 -59.71 REMARK 500 1 ARG A 698 -13.37 -166.23 REMARK 500 1 LYS A 700 46.76 -60.91 REMARK 500 1 ASP A 701 -39.00 -142.12 REMARK 500 1 ALA A 703 52.14 -64.82 REMARK 500 1 ASN A 712 71.10 47.52 REMARK 500 1 VAL A 713 17.50 46.45 REMARK 500 1 ALA A 723 -70.83 -157.64 REMARK 500 1 GLU A 724 34.75 -86.46 REMARK 500 1 GLU A 731 -6.22 -48.65 REMARK 500 1 ALA A 734 122.25 -178.89 REMARK 500 1 THR A 759 -164.03 -170.05 REMARK 500 1 LEU A 761 79.33 -67.23 REMARK 500 1 VAL B 341 -148.16 -160.06 REMARK 500 1 GLU B 343 -82.00 -56.22 REMARK 500 1 SER B 344 80.01 171.23 REMARK 500 2 MET A 663 -59.14 62.29 REMARK 500 2 ASP A 665 52.94 -64.69 REMARK 500 2 ARG A 678 -70.44 -55.65 REMARK 500 2 GLN A 697 -76.91 -112.63 REMARK 500 2 ARG A 698 -154.52 50.94 REMARK 500 2 VAL A 699 -152.84 39.70 REMARK 500 2 LYS A 700 -8.45 -150.51 REMARK 500 2 VAL A 713 20.46 46.61 REMARK 500 2 ALA A 723 -71.13 -169.02 REMARK 500 2 GLU A 724 36.95 -76.46 REMARK 500 2 ALA A 734 129.14 -179.00 REMARK 500 2 LEU A 757 103.95 -40.17 REMARK 500 2 ASP A 758 72.57 -117.82 REMARK 500 2 THR A 759 -164.73 -167.09 REMARK 500 2 LEU A 761 83.75 -65.74 REMARK 500 2 THR B 339 53.36 -67.47 REMARK 500 2 GLU B 343 -86.50 -69.31 REMARK 500 2 SER B 344 75.42 178.95 REMARK 500 2 PRO B 345 -40.93 -28.03 REMARK 500 2 ALA B 347 -72.01 -119.69 REMARK 500 2 ASP B 348 87.13 72.11 REMARK 500 2 PRO B 349 48.77 -70.25 REMARK 500 3 GLN A 664 -54.17 67.95 REMARK 500 3 ASP A 665 91.31 -1.75 REMARK 500 3 ARG A 698 152.24 85.15 REMARK 500 3 VAL A 699 49.55 -63.16 REMARK 500 3 LYS A 700 136.38 179.61 REMARK 500 3 ALA A 702 33.55 -162.69 REMARK 500 3 ALA A 706 126.71 176.28 REMARK 500 3 VAL A 713 20.36 45.02 REMARK 500 3 ALA A 723 -80.76 -163.10 REMARK 500 REMARK 500 THIS ENTRY HAS 457 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19423 RELATED DB: BMRB DBREF 2MC1 A 664 767 UNP P15498 VAV_HUMAN 664 767 DBREF 2MC1 B 338 350 UNP P48025 KSYK_MOUSE 338 350 SEQADV 2MC1 GLY A 661 UNP P15498 EXPRESSION TAG SEQADV 2MC1 HIS A 662 UNP P15498 EXPRESSION TAG SEQADV 2MC1 MET A 663 UNP P15498 EXPRESSION TAG SEQRES 1 A 107 GLY HIS MET GLN ASP LEU SER VAL HIS LEU TRP TYR ALA SEQRES 2 A 107 GLY PRO MET GLU ARG ALA GLY ALA GLU SER ILE LEU ALA SEQRES 3 A 107 ASN ARG SER ASP GLY THR PHE LEU VAL ARG GLN ARG VAL SEQRES 4 A 107 LYS ASP ALA ALA GLU PHE ALA ILE SER ILE LYS TYR ASN SEQRES 5 A 107 VAL GLU VAL LYS HIS ILE LYS ILE MET THR ALA GLU GLY SEQRES 6 A 107 LEU TYR ARG ILE THR GLU LYS LYS ALA PHE ARG GLY LEU SEQRES 7 A 107 THR GLU LEU VAL GLU PHE TYR GLN GLN ASN SER LEU LYS SEQRES 8 A 107 ASP CYS PHE LYS SER LEU ASP THR THR LEU GLN PHE PRO SEQRES 9 A 107 PHE LYS GLU SEQRES 1 B 13 ASP THR GLU VAL TYR GLU SER PRO PTR ALA ASP PRO GLU MODRES 2MC1 PTR B 346 TYR O-PHOSPHOTYROSINE HET PTR B 346 24 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P HELIX 1 1 ASP A 665 HIS A 669 5 5 HELIX 2 2 GLU A 677 ARG A 688 1 12 HELIX 3 3 GLY A 737 GLN A 746 1 10 HELIX 4 4 GLN A 747 ASN A 748 5 2 HELIX 5 5 SER A 749 CYS A 753 5 5 SHEET 1 A 4 TYR A 672 GLY A 674 0 SHEET 2 A 4 THR A 692 ARG A 696 1 O VAL A 695 N ALA A 673 SHEET 3 A 4 PHE A 705 TYR A 711 -1 O LYS A 710 N THR A 692 SHEET 4 A 4 GLU A 714 ILE A 720 -1 O GLU A 714 N TYR A 711 SHEET 1 B 3 TYR A 672 GLY A 674 0 SHEET 2 B 3 THR A 692 ARG A 696 1 O VAL A 695 N ALA A 673 SHEET 3 B 3 PHE A 763 PRO A 764 1 O PHE A 763 N PHE A 693 LINK C PRO B 345 N PTR B 346 1555 1555 1.34 LINK C PTR B 346 N ALA B 347 1555 1555 1.33 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