HEADER MEMBRANE PROTEIN 29-JUN-99 1QTS TITLE CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT (ALPHA-ADAPTIN C); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938; COMPND 5 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 OTHER_DETAILS: MUS MUSCULUS KEYWDS MEMBRANE PROTEIN, FOUR-WAVELENGTH MAD, SELENOMETHIONINE EXPDTA X-RAY DIFFRACTION AUTHOR L.M.TRAUB,M.A.DOWNS,J.L.WESTRICH,D.H.FREMONT REVDAT 6 14-FEB-24 1QTS 1 SEQADV REVDAT 5 24-FEB-09 1QTS 1 VERSN REVDAT 4 01-APR-03 1QTS 1 JRNL REVDAT 3 23-JUN-00 1QTS 1 SOURCE REMARK DBREF SEQADV REVDAT 2 31-AUG-99 1QTS 1 JRNL REVDAT 1 12-JUL-99 1QTS 0 JRNL AUTH L.M.TRAUB,M.A.DOWNS,J.L.WESTRICH,D.H.FREMONT JRNL TITL CRYSTAL STRUCTURE OF THE ALPHA APPENDAGE OF AP-2 REVEALS A JRNL TITL 2 RECRUITMENT PLATFORM FOR CLATHRIN-COAT ASSEMBLY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 96 8907 1999 JRNL REFN ISSN 0027-8424 JRNL PMID 10430869 JRNL DOI 10.1073/PNAS.96.16.8907 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 45632 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2291 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.940 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.560 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QTS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-99. REMARK 100 THE DEPOSITION ID IS D_1000009257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M AMMONIUM SULFATE, 80 MM HEPES, REMARK 280 8% DIOXANE, PH 6.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.37450 REMARK 290 SMTRY3 2 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: 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASP A 761 O HOH A 36 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 920 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 924 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES 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 ARG A 697 75.53 -100.35 REMARK 500 ASN A 719 -158.47 -112.23 REMARK 500 GLN A 732 -132.78 57.54 REMARK 500 ASP A 760 -90.69 6.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 200 REMARK 615 HOH A 240 REMARK 615 HOH A 242 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QTP RELATED DB: PDB REMARK 900 P1-CRYSTAL FORM (SEMET) OF SAME PROTEIN RCSB ID CODE IS RCSB009255 DBREF 1QTS A 692 938 UNP P17427 AP2A2_MOUSE 692 938 SEQADV 1QTS GLY A 692 UNP P17427 SER 692 CONFLICT SEQADV 1QTS SER A 693 UNP P17427 ALA 693 CONFLICT SEQADV 1QTS PRO A 694 UNP P17427 VAL 694 CONFLICT SEQADV 1QTS GLY A 695 UNP P17427 ALA 695 CONFLICT SEQADV 1QTS ILE A 696 UNP P17427 PRO 696 CONFLICT SEQADV 1QTS ARG A 697 UNP P17427 LEU 697 CONFLICT SEQADV 1QTS LEU A 698 UNP P17427 ALA 698 CONFLICT SEQADV 1QTS GLY A 699 UNP P17427 PRO 699 CONFLICT SEQADV 1QTS SER A 700 UNP P17427 GLY 700 CONFLICT 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 FORMUL 2 HOH *244(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 N ILE A 724 O PHE A 717 SHEET 3 A 5 LEU A 734 ASN A 743 -1 O LEU A 734 N ARG A 731 SHEET 4 A 5 GLN A 782 CYS A 791 -1 O VAL A 783 N TYR A 741 SHEET 5 A 5 LEU A 766 THR A 770 -1 N ASN A 767 O GLU A 790 SHEET 1 B 3 LEU A 750 ILE A 757 0 SHEET 2 B 3 VAL A 800 TYR A 807 -1 N VAL A 800 O ILE A 757 SHEET 3 B 3 THR A 810 LYS A 817 -1 N THR A 810 O TYR A 807 SHEET 1 C 5 GLU A 849 LYS A 855 0 SHEET 2 C 5 MET A 914 THR A 921 -1 N TYR A 915 O PHE A 854 SHEET 3 C 5 GLN A 899 ASN A 909 -1 N LEU A 903 O ARG A 920 SHEET 4 C 5 PHE A 887 HIS A 894 -1 N PHE A 887 O LEU A 906 SHEET 5 C 5 PHE A 826 PRO A 828 -1 N GLN A 827 O ILE A 892 SHEET 1 C1 5 GLU A 849 LYS A 855 0 SHEET 2 C1 5 MET A 914 THR A 921 -1 N TYR A 915 O PHE A 854 SHEET 3 C1 5 GLN A 899 ASN A 909 -1 N LEU A 903 O ARG A 920 SHEET 4 C1 5 PHE A 887 HIS A 894 -1 N PHE A 887 O LEU A 906 SHEET 5 C1 5 ALA A 875 LEU A 876 -1 N ALA A 875 O ALA A 890 CRYST1 40.807 72.749 41.861 90.00 99.69 90.00 P 1 21 1 2 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 0.024506 0.000000 0.004184 0.00000 SCALE2 0.000000 0.013746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024234 0.00000