HEADER ENDOCYTOSIS/EXOCYTOSIS 05-FEB-02 1KYU TITLE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-ADAPTIN C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938; COMPND 5 SYNONYM: AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15; COMPND 9 CHAIN: P; COMPND 10 FRAGMENT: RESIDUES 628-632; COMPND 11 SYNONYM: PROTEIN EPS15, AF-1P PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL4; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 13 IS A NATURALLY OCCURING SEQUENCE IN EPS15 (MOUSE) KEYWDS PROTEIN-PEPTIDE COMPLEX, ENDOCYTOSIS, ENDOCYTOSIS-EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.J.BRETT,L.M.TRAUB,D.H.FREMONT REVDAT 4 16-AUG-23 1KYU 1 SEQADV REVDAT 3 24-FEB-09 1KYU 1 VERSN REVDAT 2 01-APR-03 1KYU 1 JRNL REVDAT 1 12-JUN-02 1KYU 0 JRNL AUTH T.J.BRETT,L.M.TRAUB,D.H.FREMONT JRNL TITL ACCESSORY PROTEIN RECRUITMENT MOTIFS IN CLATHRIN-MEDIATED JRNL TITL 2 ENDOCYTOSIS. JRNL REF STRUCTURE V. 10 797 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12057195 JRNL DOI 10.1016/S0969-2126(02)00784-0 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1127447.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 18506 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 894 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2486 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 140 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.042 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1999 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.36000 REMARK 3 B22 (A**2) : 5.15000 REMARK 3 B33 (A**2) : 5.21000 REMARK 3 B12 (A**2) : 1.12000 REMARK 3 B13 (A**2) : 4.70000 REMARK 3 B23 (A**2) : 1.45000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.080 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 56.42 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.PARAM REMARK 3 TOPOLOGY FILE 3 : ION.PARAM REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015481. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20976 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38200 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1QTP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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, P 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY P 627 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 ARG A 697 68.88 -103.88 REMARK 500 ASN A 719 -158.40 -119.51 REMARK 500 GLN A 732 -128.46 57.93 REMARK 500 PRO P 630 3.50 -62.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QTP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE REMARK 900 RELATED ID: 1QTS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE REMARK 900 RELATED ID: 1KY6 RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1KY7 RELATED DB: PDB REMARK 900 THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH REMARK 900 AMPHIPHYSIN FXDXF REMARK 900 RELATED ID: 1KYD RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1KYF RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF REMARK 900 PEPTIDE DBREF 1KYU A 701 938 UNP P17427 AP2A2_MOUSE 701 938 DBREF 1KYU P 628 632 UNP P42567 EP15_MOUSE 628 632 SEQADV 1KYU GLY A 692 UNP P17427 CLONING ARTIFACT SEQADV 1KYU SER A 693 UNP P17427 CLONING ARTIFACT SEQADV 1KYU PRO A 694 UNP P17427 CLONING ARTIFACT SEQADV 1KYU GLY A 695 UNP P17427 CLONING ARTIFACT SEQADV 1KYU ILE A 696 UNP P17427 CLONING ARTIFACT SEQADV 1KYU ARG A 697 UNP P17427 CLONING ARTIFACT SEQADV 1KYU LEU A 698 UNP P17427 CLONING ARTIFACT SEQADV 1KYU GLY A 699 UNP P17427 CLONING ARTIFACT SEQADV 1KYU SER A 700 UNP P17427 CLONING ARTIFACT SEQRES 1 A 247 GLY SER PRO GLY ILE ARG LEU GLY SER SER GLU ASP ASN SEQRES 2 A 247 PHE ALA ARG PHE VAL CYS LYS ASN ASN GLY VAL LEU PHE SEQRES 3 A 247 GLU ASN GLN LEU LEU GLN ILE GLY LEU LYS SER GLU PHE SEQRES 4 A 247 ARG GLN ASN LEU GLY ARG MET PHE ILE PHE TYR GLY ASN SEQRES 5 A 247 LYS THR SER THR GLN PHE LEU ASN PHE THR PRO THR LEU SEQRES 6 A 247 ILE CYS ALA ASP ASP LEU GLN THR ASN LEU ASN LEU GLN SEQRES 7 A 247 THR LYS PRO VAL ASP PRO THR VAL ASP GLY GLY ALA GLN SEQRES 8 A 247 VAL GLN GLN VAL VAL ASN ILE GLU CYS ILE SER ASP PHE SEQRES 9 A 247 THR GLU ALA PRO VAL LEU ASN ILE GLN PHE ARG TYR GLY SEQRES 10 A 247 GLY THR PHE GLN ASN VAL SER VAL LYS LEU PRO ILE THR SEQRES 11 A 247 LEU ASN LYS PHE PHE GLN PRO THR GLU MET ALA SER GLN SEQRES 12 A 247 ASP PHE PHE GLN ARG TRP LYS GLN LEU SER ASN PRO GLN SEQRES 13 A 247 GLN GLU VAL GLN ASN ILE PHE LYS ALA LYS HIS PRO MET SEQRES 14 A 247 ASP THR GLU ILE THR LYS ALA LYS ILE ILE GLY PHE GLY SEQRES 15 A 247 SER ALA LEU LEU GLU GLU VAL ASP PRO ASN PRO ALA ASN SEQRES 16 A 247 PHE VAL GLY ALA GLY ILE ILE HIS THR LYS THR THR GLN SEQRES 17 A 247 ILE GLY CYS LEU LEU ARG LEU GLU PRO ASN LEU GLN ALA SEQRES 18 A 247 GLN MET TYR ARG LEU THR LEU ARG THR SER LYS ASP THR SEQRES 19 A 247 VAL SER GLN ARG LEU CYS GLU LEU LEU SER GLU GLN PHE SEQRES 1 P 6 GLY SER ASP PRO PHE LYS FORMUL 3 HOH *197(H2 O) HELIX 1 1 ASN A 704 VAL A 709 5 6 HELIX 2 2 ALA A 759 ASN A 765 1 7 HELIX 3 3 THR A 821 LYS A 824 5 4 HELIX 4 4 ALA A 832 LYS A 841 1 10 HELIX 5 5 ASN A 845 GLN A 847 5 3 HELIX 6 6 ASP A 861 GLY A 873 1 13 HELIX 7 7 LYS A 923 GLU A 936 1 14 SHEET 1 A 5 GLY A 714 GLU A 718 0 SHEET 2 A 5 LEU A 722 ARG A 731 -1 O ILE A 724 N PHE A 717 SHEET 3 A 5 LEU A 734 ASN A 743 -1 O PHE A 738 N LYS A 727 SHEET 4 A 5 GLN A 782 CYS A 791 -1 O GLN A 785 N ILE A 739 SHEET 5 A 5 LEU A 766 THR A 770 -1 N GLN A 769 O ASN A 788 SHEET 1 B 3 LEU A 750 ILE A 757 0 SHEET 2 B 3 VAL A 800 TYR A 807 -1 O ASN A 802 N THR A 755 SHEET 3 B 3 THR A 810 LYS A 817 -1 O VAL A 814 N ILE A 803 SHEET 1 C 5 GLU A 849 LYS A 855 0 SHEET 2 C 5 MET A 914 THR A 921 -1 O LEU A 917 N ASN A 852 SHEET 3 C 5 GLN A 899 ASN A 909 -1 N ASN A 909 O MET A 914 SHEET 4 C 5 PHE A 887 HIS A 894 -1 N GLY A 891 O CYS A 902 SHEET 5 C 5 PHE A 826 PRO A 828 -1 N GLN A 827 O ILE A 892 SHEET 1 D 5 GLU A 849 LYS A 855 0 SHEET 2 D 5 MET A 914 THR A 921 -1 O LEU A 917 N ASN A 852 SHEET 3 D 5 GLN A 899 ASN A 909 -1 N ASN A 909 O MET A 914 SHEET 4 D 5 PHE A 887 HIS A 894 -1 N GLY A 891 O CYS A 902 SHEET 5 D 5 ALA A 875 LEU A 877 -1 N ALA A 875 O ALA A 890 CRYST1 38.670 40.750 41.890 99.67 99.95 113.28 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 0.025860 0.011126 0.007709 0.00000 SCALE2 0.000000 0.026715 0.007227 0.00000 SCALE3 0.000000 0.000000 0.025108 0.00000