HEADER ENDOCYTOSIS/EXOCYTOSIS 14-SEP-04 1W80 TITLE CRYSTAL STRUCTURE OF THE ALPHA-ADAPTIN APPENDAGE DOMAIN, FROM THE AP2 TITLE 2 ADAPTOR COMPLEX, BOUND TO 2 PEPTIDES FROM SYNAPTOJANIN170 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADAPTER-RELATED PROTEIN COMPLEX 2 ALPHA 2 SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APPENDAGE DOMAIN, RESIDUES 695-938; COMPND 5 SYNONYM: ALPHA-ADAPTIN C, ADAPTOR PROTEIN COMPLEX AP-2 ALPHA-2 COMPND 6 SUBUNIT, CLATHRIN ASSEMBLY, PROTEIN COMPLEX 2 ALPHA-C LARGE CHAIN, COMPND 7 100 KDA COATED VESICLE PROTEIN, PLASMA MEMBRANE ADAPTOR HA2/AP2 COMPND 8 ADAPTIN ALPHA C SUBUNIT, ALPHA-ADAPTIN APPENDAGE DOMAIN FROM AP2; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: SYNAPTOJANIN 1; COMPND 12 CHAIN: P; COMPND 13 FRAGMENT: PEPTIDE CONTAINING WVXF MOTIF, RESIDUES 1479-1490; COMPND 14 SYNONYM: SYNAPTIC INOSITOL-1,4,5-TRISPHOSPHATE 5-PHOSPHATASE 1, SYJ- COMPND 15 P3; COMPND 16 EC: 3.1.3.36; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 3; COMPND 19 MOLECULE: SYNAPTOJANIN 1; COMPND 20 CHAIN: Q; COMPND 21 FRAGMENT: PEPTIDE CONTAINING FXDXF MOTIF, RESIDUES 1460-1471; COMPND 22 SYNONYM: SYNAPTIC INOSITOL-1,4,5-TRISPHOSPHATE 5-PHOSPHATASE 1, SYJ- COMPND 23 P3; COMPND 24 EC: 3.1.3.36; COMPND 25 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T2; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_COMMON: HUMAN; SOURCE 19 ORGANISM_TAXID: 9606 KEYWDS ENDOCYTOSIS/EXOCYTOSIS, ENDOCYTOSIS, ALPHA-ADAPTIN APPENDAGE, ADAPTOR KEYWDS 2 COMPLEX, AP2, SYNAPTOJANIN, EXOCYTOSIS, LIPID-BINDING, ENDOCYTOSIS- KEYWDS 3 EXOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.G.J.FORD,G.J.K.PRAEFCKE,H.T.MCMAHON REVDAT 4 13-DEC-23 1W80 1 REMARK REVDAT 3 24-FEB-09 1W80 1 VERSN REVDAT 2 01-SEP-05 1W80 1 JRNL REVDAT 1 27-OCT-04 1W80 0 JRNL AUTH G.J.K.PRAEFCKE,M.G.J.FORD,E.M.SCHMID,L.E.OLESEN,J.L.GALLOP, JRNL AUTH 2 S.-Y.PEAK-CHEW,Y.VALLIS,M.M.BABU,I.G.MILLS,H.T.MCMAHON JRNL TITL EVOLVING NATURE OF THE AP2 ALPHA-APPENDAGE HUB DURING JRNL TITL 2 CLATHRIN-COATED VESICLE ENDOCYTOSIS. JRNL REF EMBO J. V. 23 4371 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15496985 JRNL DOI 10.1038/SJ.EMBOJ.7600445 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 27464 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1467 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1434 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2096 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 277 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.63000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -2.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.89000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.451 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2204 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1950 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2983 ; 2.238 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4571 ; 1.013 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 269 ; 6.701 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;39.184 ;25.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 376 ;13.341 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.341 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 330 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2464 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 438 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 393 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1956 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1059 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1392 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.246 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.194 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 48 ; 0.295 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.192 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1723 ; 1.927 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2180 ; 2.246 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 960 ; 3.644 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 803 ; 5.076 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 1W80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1290021049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE (220), DOUBLE REMARK 200 CRYSTAL FOCUSSING MONOCHROMATOR REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28939 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : 0.87000 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1B9K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M AMMONIUM SULFATE, 3% ISOPROPANOL, REMARK 280 0.05M SODIUM CITRATE, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 73.29950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.66100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.29950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.66100 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, Q 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 400 REMARK 400 COMPOUND REMARK 400 CATALYSES THE FOLLOWING REACTION: REMARK 400 1-PHOSPHATIDYL-1D-MYO-INOSITOL 4,5-BISPHOSPHATE + H2O --> REMARK 400 1-PHOSPHATIDYL-1D-MYO-INOSITOL 4-PHOSPHATE + PHOSPHATE. 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 A 689 REMARK 465 SER A 690 REMARK 465 ASN P 1 REMARK 465 GLU P 10 REMARK 465 GLU P 11 REMARK 465 GLU P 12 REMARK 465 LEU Q 1 REMARK 465 LEU Q 10 REMARK 465 GLN Q 11 REMARK 465 GLY Q 12 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 OD2 ASP A 835 O HOH A 2154 2.11 REMARK 500 O HOH A 2208 O HOH A 2209 2.11 REMARK 500 OE1 GLU A 729 O2 DTD A 1943 2.14 REMARK 500 OE1 GLN A 847 O HOH A 2166 2.16 REMARK 500 NE2 GLN A 928 O HOH A 2238 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 729 CB GLU A 729 CG -0.140 REMARK 500 GLU A 879 CG GLU A 879 CD 0.106 REMARK 500 LYS A 896 CE LYS A 896 NZ 0.151 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 ASP A 794 CB - CG - OD1 ANGL. DEV. = -6.7 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 ASN A 719 -158.23 -132.49 REMARK 500 GLN A 732 -132.50 51.12 REMARK 500 LEU A 843 51.44 -108.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2022 DISTANCE = 6.16 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 A1940 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 A1941 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 A1942 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1944 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A1939 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTD A1943 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B9K RELATED DB: PDB REMARK 900 ALPHA-ADAPTIN APPENDAGE DOMAIN, FROM CLATHRIN ADAPTOR AP2 REMARK 900 RELATED ID: 1GW5 RELATED DB: PDB REMARK 900 AP2 CLATHRIN ADAPTOR CORE REMARK 900 RELATED ID: 1KY6 RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSINDPW REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1KY7 RELATED DB: PDB REMARK 900 THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX REMARK 900 WITHAMPHIPHYSIN FXDXF REMARK 900 RELATED ID: 1KYD RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSINDPW REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1KYF RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15DPF REMARK 900 PEPTIDE REMARK 900 RELATED ID: 1KYU RELATED DB: PDB REMARK 900 AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15DPF REMARK 900 PEPTIDE 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 999 REMARK 999 SEQUENCE REMARK 999 AT RESIDUES 889 AND 890 FOR CHAIN A, THE SEQUENCE IN REMARK 999 THE COORDINATES DISAGREES WITH THE UNIPROT ENTRY. THE REMARK 999 SEQUENCE IN THE COORDINATES (GLY-ALA) AGREES WITH THE REMARK 999 ELECTRON DENSITY AND SEQUENCING EXPERIMENTS. REMARK 999 REMARK 999 THE FIRST THREE RESIDUES FOR WHICH DENSITY IS OBSERVED REMARK 999 FOR CHAIN A (PRO-GLY-ILE) ARE FROM THE EXPRESSION VECTOR REMARK 999 (PGEX-4T2). THIS IS PRECEEDED BY GLY-SER FOR WHICH NO REMARK 999 DENSITY IS OBSERVED. PRO-ILE-GLY IS FOLLOWED BY A LEU REMARK 999 WHICH WAS INTRODUCED IN THE CLONING PRIMER. THE SEQUENCE REMARK 999 FOLLOWING THIS RESIDUE MATCHES UNIPROT REFERENCE P17427. DBREF 1W80 A 689 694 PDB 1W80 1W80 689 694 DBREF 1W80 A 695 938 UNP P17427 A2A2_MOUSE 695 938 DBREF 1W80 P 1 12 UNP O43426 SYJ1_HUMAN 1479 1490 DBREF 1W80 Q 1 12 UNP O43426 SYJ1_HUMAN 1460 1471 SEQADV 1W80 GLY A 889 UNP P17247 VAL 889 CONFLICT SEQADV 1W80 ALA A 890 UNP P17247 LEU 889 CONFLICT SEQRES 1 A 250 GLY SER PRO GLY ILE LEU ALA PRO LEU ALA PRO GLY SER SEQRES 2 A 250 GLU ASP ASN PHE ALA ARG PHE VAL CYS LYS ASN ASN GLY SEQRES 3 A 250 VAL LEU PHE GLU ASN GLN LEU LEU GLN ILE GLY LEU LYS SEQRES 4 A 250 SER GLU PHE ARG GLN ASN LEU GLY ARG MET PHE ILE PHE SEQRES 5 A 250 TYR GLY ASN LYS THR SER THR GLN PHE LEU ASN PHE THR SEQRES 6 A 250 PRO THR LEU ILE CYS ALA ASP ASP LEU GLN THR ASN LEU SEQRES 7 A 250 ASN LEU GLN THR LYS PRO VAL ASP PRO THR VAL ASP GLY SEQRES 8 A 250 GLY ALA GLN VAL GLN GLN VAL ILE ASN ILE GLU CYS ILE SEQRES 9 A 250 SER ASP PHE THR GLU ALA PRO VAL LEU ASN ILE GLN PHE SEQRES 10 A 250 ARG TYR GLY GLY THR PHE GLN ASN VAL SER VAL LYS LEU SEQRES 11 A 250 PRO ILE THR LEU ASN LYS PHE PHE GLN PRO THR GLU MET SEQRES 12 A 250 ALA SER GLN ASP PHE PHE GLN ARG TRP LYS GLN LEU SER SEQRES 13 A 250 ASN PRO GLN GLN GLU VAL GLN ASN ILE PHE LYS ALA LYS SEQRES 14 A 250 HIS PRO MET ASP THR GLU ILE THR LYS ALA LYS ILE ILE SEQRES 15 A 250 GLY PHE GLY SER ALA LEU LEU GLU GLU VAL ASP PRO ASN SEQRES 16 A 250 PRO ALA ASN PHE VAL GLY ALA GLY ILE ILE HIS THR LYS SEQRES 17 A 250 THR THR GLN ILE GLY CYS LEU LEU ARG LEU GLU PRO ASN SEQRES 18 A 250 LEU GLN ALA GLN MET TYR ARG LEU THR LEU ARG THR SER SEQRES 19 A 250 LYS ASP THR VAL SER GLN ARG LEU CYS GLU LEU LEU SER SEQRES 20 A 250 GLU GLN PHE SEQRES 1 P 12 ASN PRO LYS GLY TRP VAL THR PHE GLU GLU GLU GLU SEQRES 1 Q 12 LEU ASP GLY PHE LYS ASP SER PHE ASP LEU GLN GLY HET BEN A1939 9 HET CO3 A1940 4 HET CO3 A1941 4 HET CO3 A1942 4 HET DTD A1943 8 HET SO4 A1944 5 HETNAM BEN BENZAMIDINE HETNAM CO3 CARBONATE ION HETNAM DTD DITHIANE DIOL HETNAM SO4 SULFATE ION FORMUL 4 BEN C7 H8 N2 FORMUL 5 CO3 3(C O3 2-) FORMUL 8 DTD C4 H8 O2 S2 FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *277(H2 O) HELIX 1 1 GLY A 700 ARG A 707 1 8 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 LEU A 843 1 12 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 AA 5 ASN A 713 GLU A 718 0 SHEET 2 AA 5 LEU A 722 ARG A 731 -1 O ILE A 724 N LEU A 716 SHEET 3 AA 5 LEU A 734 ASN A 743 -1 O LEU A 734 N ARG A 731 SHEET 4 AA 5 GLN A 782 CYS A 791 -1 O VAL A 783 N TYR A 741 SHEET 5 AA 5 LEU A 766 GLN A 769 -1 O ASN A 767 N GLU A 790 SHEET 1 AB 3 PHE A 749 ILE A 757 0 SHEET 2 AB 3 VAL A 800 TYR A 807 -1 O VAL A 800 N ILE A 757 SHEET 3 AB 3 THR A 810 LYS A 817 -1 O THR A 810 N TYR A 807 SHEET 1 AC 3 PHE A 826 PRO A 828 0 SHEET 2 AC 3 PHE A 887 HIS A 894 -1 O ILE A 892 N GLN A 827 SHEET 3 AC 3 ALA A 875 LEU A 877 -1 O ALA A 875 N ALA A 890 SHEET 1 AD 5 PHE A 826 PRO A 828 0 SHEET 2 AD 5 PHE A 887 HIS A 894 -1 O ILE A 892 N GLN A 827 SHEET 3 AD 5 GLN A 899 ASN A 909 -1 O ILE A 900 N ILE A 893 SHEET 4 AD 5 MET A 914 THR A 921 -1 O MET A 914 N ASN A 909 SHEET 5 AD 5 GLU A 849 LYS A 855 -1 O VAL A 850 N LEU A 919 SITE 1 AC1 4 ARG A 731 LYS A 841 ARG A 920 LYS Q 5 SITE 1 AC2 2 ARG A 731 GLN A 732 SITE 1 AC3 3 ASN A 719 GLN A 720 HOH A2262 SITE 1 AC4 5 GLY A 700 SER A 701 GLU A 702 ASP A 703 SITE 2 AC4 5 HOH A2263 SITE 1 AC5 9 ARG A 839 HIS A 858 PRO A 859 GLY A 891 SITE 2 AC5 9 GLY A 901 CYS A 902 LEU A 903 HOH A2159 SITE 3 AC5 9 HOH A2261 SITE 1 AC6 5 GLU A 729 GLY A 735 GLU A 849 HOH A2059 SITE 2 AC6 5 HOH Q2003 CRYST1 146.599 67.322 39.721 90.00 94.53 90.00 C 1 2 1 4 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 0.006821 0.000000 0.000540 0.00000 SCALE2 0.000000 0.014854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025254 0.00000