HEADER PEPTIDE BINDING PROTEIN 25-APR-08 2ROZ TITLE STRUCTURE OF THE C-TERMINAL PID DOMAIN OF FE65L1 COMPLEXED WITH THE TITLE 2 CYTOPLASMIC TAIL OF APP REVEALS A NOVEL PEPTIDE BINDING MODE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE FROM AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APP-DERIVED_32-MER_PEPTIDE; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER COMPND 8 2; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: C-TERMINAL PID DOMAIN; COMPND 11 SYNONYM: FE65L1; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICAL SYNTHESIS; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 6 ORGANISM_COMMON: MOUSE; SOURCE 7 ORGANISM_TAXID: 10090; SOURCE 8 GENE: APBB2; SOURCE 9 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 10 OTHER_DETAILS: E. COLI CELL-FREE KEYWDS FE65L1, PID DOMAIN, AMYLOID PRECURSOR PROTEIN, ALTERNATIVE SPLICING, KEYWDS 2 AMYLOID, APOPTOSIS, CELL ADHESION, COATED PIT, COPPER, ENDOCYTOSIS, KEYWDS 3 GLYCOPROTEIN, HEPARIN-BINDING, IRON, MEMBRANE, METAL-BINDING, NOTCH KEYWDS 4 SIGNALING PATHWAY, PHOSPHOPROTEIN, PROTEASE INHIBITOR, SERINE KEYWDS 5 PROTEASE INHIBITOR, TRANSMEMBRANE, ZINC, STRUCTURAL GENOMICS, KEYWDS 6 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 7 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 8 PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.LI,S.KOSHIBA,N.TOCHIO,S.WATANABE,T.HARADA,M.INOUE,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 16-MAR-22 2ROZ 1 REMARK SEQADV REVDAT 3 23-DEC-08 2ROZ 1 SOURCE VERSN REVDAT 2 04-NOV-08 2ROZ 1 JRNL REVDAT 1 22-JUL-08 2ROZ 0 JRNL AUTH H.LI,S.KOSHIBA,F.HAYASHI,N.TOCHIO,T.TOMIZAWA,T.KASAI, JRNL AUTH 2 T.YABUKI,Y.MOTODA,T.HARADA,S.WATANABE,M.INOUE,Y.HAYASHIZAKI, JRNL AUTH 3 A.TANAKA,T.KIGAWA,S.YOKOYAMA JRNL TITL STRUCTURE OF THE C-TERMINAL PHOSPHOTYROSINE INTERACTION JRNL TITL 2 DOMAIN OF FE65L1 COMPLEXED WITH THE CYTOPLASMIC TAIL OF JRNL TITL 3 AMYLOID PRECURSOR PROTEIN REVEALS A NOVEL PEPTIDE BINDING JRNL TITL 4 MODE JRNL REF J.BIOL.CHEM. V. 283 27165 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18650440 JRNL DOI 10.1074/JBC.M803892200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 1.0.8 REMARK 3 AUTHORS : BRUKER (XWINNMR), HERRMANN, GUNTERT AND WUTHRICH REMARK 3 (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ROZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000150110. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.37MM [U-13C; U-15N] FE65L1 REMARK 210 PID2, 0.37MM APP-DERIVED 32-MER REMARK 210 PEPTIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D_13C,15N F1-FILTERED REMARK 210 13C F3-EDITED NOESY; 3D_13C,15N REMARK 210 F1-FILTERED 15N F3-EDITED NOESY; REMARK 210 2D_F2 13C,15N- FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9820, CYANA 1.0.8 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE EXPERIMENTS OF THE CONVENTIONAL NOESY SPECTRA, 3D 1H REMARK 210 -15N NOESY AND 3D 1H-13C NOESY, ARE CONDUCTED AT 900 MHZ BRUKER REMARK 210 AVANCE MACHINE. HOWEVER, THE OTHER THREE FILTER-RELATED REMARK 210 EXPERIMENTS, 3D_13C,15N F1-FILTERED 13C F3-EDITED NOESY, 3D_13C, REMARK 210 15N F1-FILTERED 15N F3-EDITED NOESY, AND 2D_F2 13C,15N- FILTERED REMARK 210 NOESY, ARE CONDUCTED AT 800 MHZ BRUKER AVANCE MACHINE. 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 O SER B 123 H GLN B 127 1.51 REMARK 500 O ASN B 121 H ALA B 125 1.55 REMARK 500 H ASN B 59 O THR B 66 1.55 REMARK 500 HE21 GLN B 21 O TRP B 53 1.56 REMARK 500 O ASN B 43 H SER B 47 1.57 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 GLN A 16 -86.29 -123.43 REMARK 500 1 LYS A 25 75.71 65.32 REMARK 500 1 PHE A 27 135.00 -37.58 REMARK 500 1 GLU A 28 158.51 63.16 REMARK 500 1 GLN A 29 100.67 66.52 REMARK 500 1 SER B 3 161.80 178.81 REMARK 500 1 LYS B 17 145.58 66.90 REMARK 500 1 SER B 47 -85.59 -37.48 REMARK 500 1 ALA B 61 -157.92 -103.89 REMARK 500 1 ALA B 63 66.61 -155.07 REMARK 500 1 LYS B 71 -75.86 -61.31 REMARK 500 1 GLU B 74 32.31 -99.68 REMARK 500 1 LEU B 77 -50.82 -122.79 REMARK 500 1 ASN B 105 -166.99 -57.44 REMARK 500 1 ALA B 119 44.93 -105.02 REMARK 500 1 VAL B 122 -70.31 -54.13 REMARK 500 1 SER B 131 -40.32 178.66 REMARK 500 1 SER B 134 106.20 55.92 REMARK 500 2 ALA A 3 98.32 62.59 REMARK 500 2 THR A 5 150.07 -41.88 REMARK 500 2 SER A 12 -30.41 -39.56 REMARK 500 2 PHE A 26 46.81 -83.09 REMARK 500 2 PHE A 27 92.10 45.25 REMARK 500 2 GLN A 29 74.50 53.36 REMARK 500 2 SER B 3 97.77 -61.97 REMARK 500 2 SER B 5 116.59 -170.50 REMARK 500 2 LYS B 11 131.44 62.68 REMARK 500 2 LYS B 17 152.32 65.32 REMARK 500 2 VAL B 20 -168.11 -129.07 REMARK 500 2 TRP B 53 109.68 -49.22 REMARK 500 2 ALA B 61 -153.39 -108.95 REMARK 500 2 LYS B 71 -77.91 -61.57 REMARK 500 2 LEU B 85 152.24 -39.63 REMARK 500 2 ASN B 105 -171.18 52.46 REMARK 500 2 ALA B 119 31.76 -92.82 REMARK 500 2 SER B 131 -75.27 -42.25 REMARK 500 3 ALA A 2 -57.62 -132.37 REMARK 500 3 ALA A 3 76.51 57.54 REMARK 500 3 ASN A 17 -61.89 69.82 REMARK 500 3 LYS A 25 86.24 -156.20 REMARK 500 3 PHE A 27 94.10 44.29 REMARK 500 3 GLU A 28 44.85 -99.60 REMARK 500 3 GLN A 29 96.08 61.99 REMARK 500 3 GLN A 31 156.33 60.06 REMARK 500 3 SER B 2 140.54 66.93 REMARK 500 3 SER B 6 -157.40 -161.64 REMARK 500 3 LYS B 17 149.76 63.71 REMARK 500 3 ARG B 19 97.30 -60.93 REMARK 500 3 VAL B 20 -162.50 -123.26 REMARK 500 3 ASP B 29 -50.70 -123.80 REMARK 500 REMARK 500 THIS ENTRY HAS 439 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED DBREF 2ROZ A 1 32 UNP P12023 A4_MOUSE 739 770 DBREF 2ROZ B 8 130 UNP Q9DBR4 APBB2_MOUSE 582 704 SEQADV 2ROZ GLY B 1 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 2 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 3 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ GLY B 4 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 5 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 6 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ GLY B 7 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 131 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ GLY B 132 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ PRO B 133 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 134 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ SER B 135 UNP Q9DBR4 EXPRESSION TAG SEQADV 2ROZ GLY B 136 UNP Q9DBR4 EXPRESSION TAG SEQRES 1 A 32 ASP ALA ALA VAL THR PRO GLU GLU ARG HIS LEU SER LYS SEQRES 2 A 32 MET GLN GLN ASN GLY TYR GLU ASN PRO THR TYR LYS PHE SEQRES 3 A 32 PHE GLU GLN MET GLN ASN SEQRES 1 B 136 GLY SER SER GLY SER SER GLY PRO THR PRO LYS THR GLU SEQRES 2 B 136 LEU VAL GLN LYS PHE ARG VAL GLN TYR LEU GLY MET LEU SEQRES 3 B 136 PRO VAL ASP ARG PRO VAL GLY MET ASP THR LEU ASN SER SEQRES 4 B 136 ALA ILE GLU ASN LEU MET THR SER SER SER LYS GLU ASP SEQRES 5 B 136 TRP PRO SER VAL ASN MET ASN VAL ALA ASP ALA THR VAL SEQRES 6 B 136 THR VAL ILE SER GLU LYS ASN GLU GLU GLU VAL LEU VAL SEQRES 7 B 136 GLU CYS ARG VAL ARG PHE LEU SER PHE MET GLY VAL GLY SEQRES 8 B 136 LYS ASP VAL HIS THR PHE ALA PHE ILE MET ASP THR GLY SEQRES 9 B 136 ASN GLN ARG PHE GLU CYS HIS VAL PHE TRP CYS GLU PRO SEQRES 10 B 136 ASN ALA ALA ASN VAL SER GLU ALA VAL GLN ALA ALA CYS SEQRES 11 B 136 SER GLY PRO SER SER GLY HELIX 1 1 PRO A 6 GLN A 15 1 10 HELIX 2 2 MET B 34 SER B 47 1 14 HELIX 3 3 ALA B 120 CYS B 130 1 11 SHEET 1 A 8 VAL B 76 ARG B 81 0 SHEET 2 A 8 THR B 64 ILE B 68 -1 SHEET 3 A 8 SER B 55 ALA B 61 -1 SHEET 4 A 8 GLN B 16 PRO B 27 -1 SHEET 5 A 8 PHE B 108 TRP B 114 -1 SHEET 6 A 8 PHE B 97 ASP B 102 -1 SHEET 7 A 8 LEU B 85 GLY B 89 -1 SHEET 8 A 8 TYR A 19 GLU A 20 -1 CISPEP 1 GLU B 116 PRO B 117 1 0.04 CISPEP 2 GLU B 116 PRO B 117 2 -0.05 CISPEP 3 GLU B 116 PRO B 117 3 0.05 CISPEP 4 GLU B 116 PRO B 117 4 0.01 CISPEP 5 GLU B 116 PRO B 117 5 -0.03 CISPEP 6 GLU B 116 PRO B 117 6 0.09 CISPEP 7 GLU B 116 PRO B 117 7 0.06 CISPEP 8 GLU B 116 PRO B 117 8 -0.08 CISPEP 9 GLU B 116 PRO B 117 9 0.00 CISPEP 10 GLU B 116 PRO B 117 10 0.02 CISPEP 11 GLU B 116 PRO B 117 11 0.06 CISPEP 12 GLU B 116 PRO B 117 12 -0.07 CISPEP 13 GLU B 116 PRO B 117 13 0.00 CISPEP 14 GLU B 116 PRO B 117 14 0.06 CISPEP 15 GLU B 116 PRO B 117 15 0.02 CISPEP 16 GLU B 116 PRO B 117 16 0.00 CISPEP 17 GLU B 116 PRO B 117 17 0.00 CISPEP 18 GLU B 116 PRO B 117 18 0.04 CISPEP 19 GLU B 116 PRO B 117 19 0.03 CISPEP 20 GLU B 116 PRO B 117 20 -0.03 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20