PDB Short entry for 2RQU HEADER SIGNALING PROTEIN 14-DEC-09 2RQU TITLE SOLUTION STRUCTURE OF THE COMPLEX BETWEEN THE DDEF1 SH3 DOMAIN AND THE TITLE 2 APC SAMP1 MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: DDEF1_SH3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1069-1129; COMPND 5 SYNONYM: DDEF1_SH3, 130 KDA PHOSPHATIDYLINOSITOL 4,5-BIPHOSPHATE- COMPND 6 DEPENDENT ARF1 GTPASE-ACTIVATING PROTEIN, PIP2-DEPENDENT ARF1 GAP, COMPND 7 ADP-RIBOSYLATION FACTOR-DIRECTED GTPASE-ACTIVATING PROTEIN 1, ARF COMPND 8 GTPASE-ACTIVATING PROTEIN 1, DEVELOPMENT AND DIFFERENTIATION- COMPND 9 ENHANCING FACTOR 1, DIFFERENTIATION-ENHANCING FACTOR 1, DEF-1; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: 19-MER FROM ADENOMATOUS POLYPOSIS COLI PROTEIN; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: UNP RESIDUES 1578-1596; COMPND 15 SYNONYM: PROTEIN APC, DELETED IN POLYPOSIS 2.5; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: PET32A; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: APC, DP2.5; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VECTOR: PET32A KEYWDS SH3 DOMAIN, GAP, SAMP MOTIF, TUMOR SUPPRESSOR, CELL JUNCTION, DISEASE KEYWDS 2 MUTATION, PHOSPHOPROTEIN, WNT SIGNALING PATHWAY, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.KAIEDA,C.MATSUI,Y.MIMORI-KIYOSUE,T.IKEGAMI REVDAT 2 01-MAY-24 2RQU 1 REMARK REVDAT 1 07-JUL-10 2RQU 0 JRNL AUTH S.KAIEDA,C.MATSUI,Y.MIMORI-KIYOSUE,T.IKEGAMI JRNL TITL STRUCTURAL BASIS OF THE RECOGNITION OF THE SAMP MOTIF OF JRNL TITL 2 ADENOMATOUS POLYPOSIS COLI BY THE SRC-HOMOLOGY 3 DOMAIN. JRNL REF BIOCHEMISTRY V. 49 5143 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20509626 JRNL DOI 10.1021/BI100563Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, ARIA 2.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), RIEPING, HABECK, REMARK 3 BARDIAUX, BERNARD, MALLIAVIN, AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000150176. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-15N] DDEF1 SH3-1, 0.5 REMARK 210 MM [U-15N] APC SAMP1-2, 5 MM REMARK 210 SODIUM PHOSPHATE-3, 5 MM [U-2H] REMARK 210 DTT-4, 0.02 % SODIUM AZIDE-5, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-13C; U- REMARK 210 15N] DDEF1 SH3-6, 0.5 MM [U-13C; REMARK 210 U-15N] APC SAMP1-7, 5 MM SODIUM REMARK 210 PHOSPHATE-8, 5 MM [U-2H] DTT-9, REMARK 210 0.02 % SODIUM AZIDE-10, 90% H2O/ REMARK 210 10% D2O; 0.5 MM [U-13C; U-15N] REMARK 210 DDEF1 SH3-11, 0.5 MM [U-13C; U- REMARK 210 15N] APC SAMP1-12, 5 MM SODIUM REMARK 210 PHOSPHATE-13, 5 MM [U-2H] DTT-14, REMARK 210 0.02 % SODIUM PHOSPHATE-15, 100% REMARK 210 D2O; 0.5 MM [U-15% 13C; U-15N] REMARK 210 DDEF1 SH3-16, 0.5 MM [U-15% 13C; REMARK 210 U-15N] APC SAMP1-17, 5 MM SODIUM REMARK 210 PHOSPHATE-18, 5 MM [U-2H] DTT-19, REMARK 210 0.02 % SODIUM AZIDE-20, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D HBHA(CO)NH; 3D MQ-HCCH-TOCSY; REMARK 210 3D HCCH-TOCSY; 3D 15N-EDITED REMARK 210 NOESY; 3D ALIPHATIC 13C-EDITED REMARK 210 NOESY; 3D AROMATIC 13C-EDITED REMARK 210 NOESY; 2D 1H-13C HSQC; 2D 1H-13C REMARK 210 CT-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY 3.115, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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 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 LEU A1127 54.29 -98.41 REMARK 500 1 SER B1581 -142.67 46.59 REMARK 500 1 LYS B1586 107.96 -59.97 REMARK 500 1 SER B1588 116.88 66.80 REMARK 500 1 PRO B1594 93.29 -63.56 REMARK 500 2 SER B1581 -154.75 56.61 REMARK 500 2 SER B1588 95.88 62.70 REMARK 500 2 PRO B1594 44.64 -88.88 REMARK 500 3 ASN A1082 -168.24 -129.89 REMARK 500 3 GLU A1100 -36.60 -131.10 REMARK 500 3 LEU A1127 -72.56 -109.73 REMARK 500 3 SER B1581 -148.54 75.41 REMARK 500 3 LYS B1586 102.38 -59.59 REMARK 500 3 SER B1588 140.63 67.83 REMARK 500 3 ALA B1595 39.46 -80.00 REMARK 500 4 SER B1581 -152.82 55.62 REMARK 500 4 LYS B1586 103.53 -55.05 REMARK 500 4 SER B1587 24.90 -77.75 REMARK 500 4 SER B1588 125.88 63.27 REMARK 500 4 PRO B1594 84.80 -66.12 REMARK 500 5 ASP A1084 77.40 -103.63 REMARK 500 5 GLU A1100 -50.61 -122.91 REMARK 500 5 SER B1581 -138.59 44.55 REMARK 500 5 LYS B1586 97.12 -63.43 REMARK 500 5 SER B1587 21.00 -72.42 REMARK 500 5 SER B1588 125.58 65.08 REMARK 500 5 LYS B1592 106.69 -51.10 REMARK 500 5 ALA B1595 73.42 64.73 REMARK 500 6 GLU A1100 -45.16 -130.03 REMARK 500 6 LEU A1127 52.04 -114.55 REMARK 500 6 SER B1581 -143.51 51.07 REMARK 500 6 LYS B1586 93.05 -68.37 REMARK 500 6 SER B1587 24.89 -77.19 REMARK 500 6 SER B1588 134.36 65.20 REMARK 500 6 PRO B1594 89.45 -63.13 REMARK 500 7 LEU A1127 -62.31 -104.77 REMARK 500 7 SER B1581 -154.31 56.66 REMARK 500 7 SER B1588 150.11 65.77 REMARK 500 7 ALA B1591 32.16 -85.20 REMARK 500 8 ASP A1084 53.29 -92.99 REMARK 500 8 SER B1581 -149.66 54.95 REMARK 500 8 LYS B1586 103.90 -59.08 REMARK 500 8 SER B1588 115.23 64.40 REMARK 500 8 PRO B1594 69.80 -67.40 REMARK 500 9 SER A1128 44.84 -92.77 REMARK 500 9 SER B1581 -152.75 53.64 REMARK 500 9 SER B1588 138.39 67.61 REMARK 500 9 PRO B1594 31.11 -73.11 REMARK 500 10 GLN A1112 84.83 -151.92 REMARK 500 10 SER B1581 -156.48 54.16 REMARK 500 REMARK 500 THIS ENTRY HAS 102 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RQT RELATED DB: PDB DBREF 2RQU A 1069 1129 UNP Q9ULH1 ASAP1_HUMAN 1069 1129 DBREF 2RQU B 1578 1596 UNP P25054 APC_HUMAN 1578 1596 SEQRES 1 A 61 VAL ARG ARG VAL LYS THR ILE TYR ASP CYS GLN ALA ASP SEQRES 2 A 61 ASN ASP ASP GLU LEU THR PHE ILE GLU GLY GLU VAL ILE SEQRES 3 A 61 ILE VAL THR GLY GLU GLU ASP GLN GLU TRP TRP ILE GLY SEQRES 4 A 61 HIS ILE GLU GLY GLN PRO GLU ARG LYS GLY VAL PHE PRO SEQRES 5 A 61 VAL SER PHE VAL HIS ILE LEU SER ASP SEQRES 1 B 19 CYS ILE ILE SER ALA MET PRO THR LYS SER SER ARG LYS SEQRES 2 B 19 ALA LYS LYS PRO ALA GLN SHEET 1 A 5 LYS A1116 PRO A1120 0 SHEET 2 A 5 TRP A1104 ILE A1109 -1 N TRP A1105 O PHE A1119 SHEET 3 A 5 VAL A1093 GLU A1099 -1 N ILE A1095 O HIS A1108 SHEET 4 A 5 ARG A1070 THR A1074 -1 N VAL A1072 O ILE A1094 SHEET 5 A 5 VAL A1124 ILE A1126 -1 O HIS A1125 N LYS A1073 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