PDB Short entry for 1U39 HEADER PROTEIN TRANSPORT 21-JUL-04 1U39 TITLE AUTO-INHIBITION MECHANISM OF X11S/MINTS FAMILY SCAFFOLD PROTEINS TITLE 2 REVEALED BY THE CLOSED CONFORMATION OF THE TANDEM PDZ DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING, FAMILY A, MEMBER COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PDZ2 DOMAIN; COMPND 6 SYNONYM: X11ALPHA/MINT1, PHOSPHOTYROSINE-BINDING/-INTERACTING DOMAIN COMPND 7 (PTB)-BEARING PROTEIN, NEURONAL MUNC18-1-INTERACTING PROTEIN 1, COMPND 8 NEURON-SPECIFIC X11 PROTEIN, ADAPTOR PROTEIN X11ALPHA; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS X11S/MINTS, PDZ DOMAIN, SCAFFOLD PROTEIN, PROTEIN TRAFFICKING, KEYWDS 2 PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 MDLTYP MINIMIZED AVERAGE AUTHOR W.FENG,J.-F.LONG,L.-N.CHAN,C.HE,A.FU,J.XIA,N.Y.IP,M.ZHANG REVDAT 4 02-MAR-22 1U39 1 REMARK REVDAT 3 24-FEB-09 1U39 1 VERSN REVDAT 2 13-SEP-05 1U39 1 JRNL REVDAT 1 26-JUL-05 1U39 0 JRNL AUTH J.-F.LONG,W.FENG,R.WANG,L.-N.CHAN,F.C.IP,J.XIA,N.Y.IP, JRNL AUTH 2 M.ZHANG JRNL TITL AUTOINHIBITION OF X11/MINT SCAFFOLD PROTEINS REVEALED BY THE JRNL TITL 2 CLOSED CONFORMATION OF THE PDZ TANDEM JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 722 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 16007100 JRNL DOI 10.1038/NSMB958 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER, A.T. (CNS), BRUNGER, A.T. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U39 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023189. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100MM POTASSIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0MM UNIFORMLY 15N LABELLED REMARK 210 PDZ2 IN 90% H2O, 10% D2O; 100MM REMARK 210 POTASSIUM PHOSPHATE; 1.0MM REMARK 210 UNIFORMLY 15N/13C LABELLED PDZ2 REMARK 210 IN 90% H2O, 10% D2O; 100MM REMARK 210 POTASSIUM PHOSPHATE; 1.0MM REMARK 210 UNIFORMLY 15N/13C LABELLED PDZ2 REMARK 210 IN 99.9% D2O; 100MM POTASSIUM REMARK 210 PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNCO, REMARK 210 HNCACB, CBCA(CO)NH; 3D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 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 ASN A 101 -68.51 65.36 REMARK 500 1 CYS A 105 -71.68 -109.59 REMARK 500 1 ARG A 109 82.74 -63.58 REMARK 500 1 VAL A 118 114.92 -37.59 REMARK 500 1 VAL A 120 101.76 -48.11 REMARK 500 1 ILE A 125 -84.51 -151.54 REMARK 500 1 ASN A 128 18.64 59.84 REMARK 500 1 ALA A 147 79.21 -103.62 REMARK 500 2 LEU A 91 30.87 -96.19 REMARK 500 2 CYS A 105 -65.62 -108.00 REMARK 500 2 ARG A 109 71.92 -67.97 REMARK 500 2 VAL A 118 -64.26 -29.58 REMARK 500 2 ARG A 119 178.70 61.71 REMARK 500 2 ILE A 125 -84.46 -137.18 REMARK 500 3 ASN A 101 -68.19 64.34 REMARK 500 3 CYS A 105 -79.48 -106.46 REMARK 500 3 LEU A 107 101.86 -174.16 REMARK 500 3 ARG A 109 78.20 -66.03 REMARK 500 3 VAL A 118 -83.31 -15.11 REMARK 500 3 ARG A 119 143.19 62.56 REMARK 500 3 ILE A 125 -86.66 -157.79 REMARK 500 3 PRO A 136 164.09 -47.92 REMARK 500 4 PHE A 97 145.14 -175.55 REMARK 500 4 CYS A 105 -67.35 -94.97 REMARK 500 4 ARG A 109 44.14 -93.40 REMARK 500 4 VAL A 118 148.80 -34.13 REMARK 500 4 ILE A 125 -84.46 -128.29 REMARK 500 4 ALA A 147 52.59 -118.06 REMARK 500 4 VAL A 148 -178.48 -53.50 REMARK 500 5 PRO A 80 88.87 -52.05 REMARK 500 5 ASP A 90 -169.17 -127.50 REMARK 500 5 CYS A 105 -84.28 -94.29 REMARK 500 5 ARG A 109 80.79 -63.89 REMARK 500 5 VAL A 118 -81.98 -15.72 REMARK 500 5 ARG A 119 129.05 63.84 REMARK 500 5 ILE A 125 -84.50 -146.07 REMARK 500 5 PRO A 136 156.97 -49.72 REMARK 500 6 ASN A 101 -70.66 64.69 REMARK 500 6 ARG A 109 91.00 -55.21 REMARK 500 6 ILE A 125 -83.02 -147.14 REMARK 500 6 PRO A 157 109.38 -50.92 REMARK 500 7 LEU A 95 -61.35 -96.98 REMARK 500 7 PHE A 97 -171.96 -176.68 REMARK 500 7 ASN A 101 -64.64 65.18 REMARK 500 7 CYS A 105 -77.73 -105.42 REMARK 500 7 VAL A 118 145.72 -31.75 REMARK 500 7 ILE A 125 -82.99 -149.38 REMARK 500 7 PRO A 136 164.20 -42.77 REMARK 500 7 ALA A 147 58.19 -116.98 REMARK 500 7 VAL A 148 173.70 -53.28 REMARK 500 REMARK 500 THIS ENTRY HAS 151 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U37 RELATED DB: PDB REMARK 900 THE SAME PROTEIN, PDZ1 DOMAIN, 20 STRUCTURES REMARK 900 RELATED ID: 1U38 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH C-PEPTIDE, 20 STRUCTURES REMARK 900 RELATED ID: 1U3B RELATED DB: PDB REMARK 900 THE SAME PROTEIN, PDZ12C DOMAIN, MINIMIZED AVERAGE STRUCTURE DBREF 1U39 A 79 158 UNP Q02410 APBA1_HUMAN 743 822 SEQRES 1 A 80 PRO PRO VAL THR THR VAL LEU ILE ARG ARG PRO ASP LEU SEQRES 2 A 80 ARG TYR GLN LEU GLY PHE SER VAL GLN ASN GLY ILE ILE SEQRES 3 A 80 CYS SER LEU MET ARG GLY GLY ILE ALA GLU ARG GLY GLY SEQRES 4 A 80 VAL ARG VAL GLY HIS ARG ILE ILE GLU ILE ASN GLY GLN SEQRES 5 A 80 SER VAL VAL ALA THR PRO HIS GLU LYS ILE VAL HIS ILE SEQRES 6 A 80 LEU SER ASN ALA VAL GLY GLU ILE HIS MET LYS THR MET SEQRES 7 A 80 PRO ALA HELIX 1 1 ILE A 112 GLY A 117 1 6 HELIX 2 2 VAL A 133 THR A 135 5 3 HELIX 3 3 PRO A 136 ASN A 146 1 11 SHEET 1 A 4 THR A 82 ARG A 87 0 SHEET 2 A 4 GLU A 150 MET A 156 -1 O ILE A 151 N ILE A 86 SHEET 3 A 4 ARG A 123 ILE A 127 -1 N ILE A 125 O LYS A 154 SHEET 4 A 4 GLN A 130 SER A 131 -1 O GLN A 130 N ILE A 127 SHEET 1 B 2 PHE A 97 GLN A 100 0 SHEET 2 B 2 ILE A 103 LEU A 107 -1 O ILE A 103 N GLN A 100 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