HEADER SIGNALING PROTEIN 10-AUG-02 1MFG TITLE THE STRUCTURE OF ERBIN PDZ DOMAIN BOUND TO THE CARBOXY- TITLE 2 TERMINAL TAIL OF THE ERBB2 RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERB-B2 INTERACTING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ERB-B2 CARBOXYL-TERMINAL FRAGMENT; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: PEPTIDE EYLGLDVPV; COMPND 10 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-KT; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: PEPTIDE SYNTHESIZED CHEMICALLY KEYWDS PDZ DOMAIN, PROTEIN-PEPTIDE COMPLEX, ERB-B2, ERBIN., KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.BIRRANE,J.CHUNG,J.A.LADIAS REVDAT 3 24-FEB-09 1MFG 1 VERSN REVDAT 2 26-AUG-08 1MFG 1 REMARK REVDAT 1 21-JAN-03 1MFG 0 JRNL AUTH G.BIRRANE,J.CHUNG,J.A.LADIAS JRNL TITL NOVEL MODE OF LIGAND RECOGNITION BY THE ERBIN PDZ JRNL TITL 2 DOMAIN JRNL REF J.BIOL.CHEM. V. 278 1399 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12444095 JRNL DOI 10.1074/JBC.C200571200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.P.BORG,S.MARCHETTO,A.LEBIVIC,V.OLLENDORFF, REMARK 1 AUTH 2 F.JAULIN-BASTARD,H.SAITO,E.FOURNIER,J.ADELAIDE, REMARK 1 AUTH 3 B.MARGOLIS,D.BIRNBAUM REMARK 1 TITL BIN: A BASOLATERAL PDZ PROTEIN THAT INTERACTS WITH REMARK 1 TITL 2 THE MAMMALIAN ERBB2/HER2 RECEPTOR REMARK 1 REF NAT.CELL BIOL. V. 2 407 2000 REMARK 1 REFN ISSN 1465-7392 REMARK 1 DOI 10.1038/35017038 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.P.LAURA,A.S.WITT,H.A.HELD,R.GERSTNER,K.DESHAYES, REMARK 1 AUTH 2 M.F.KOEHLER,K.S.KOSIK,S.S.SIDHU,L.A.LASKY REMARK 1 TITL THE ERBIN PDZ DOMAIN BINDS WITH HIGH AFFINITY AND REMARK 1 TITL 2 SPECIFICITY TO THE CARBOXYL TERMINI OF REMARK 1 TITL 3 DELTA-CATENIN AND ARVCF REMARK 1 REF J.BIOL.CHEM. V. 277 12906 2002 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M200818200 REMARK 1 REFERENCE 3 REMARK 1 AUTH Y.Z.HUANG,Q.WANG,W.C.XIONG,L.MEI REMARK 1 TITL ERBIN IS A PROTEIN CONCENTRATED AT POSTSYNAPTIC REMARK 1 TITL 2 MEMBRANES THAT INTERACTS WITH PSD-95 REMARK 1 REF J.BIOL.CHEM. V. 276 19318 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M100494200 REMARK 1 REFERENCE 4 REMARK 1 AUTH F.JAULIN-BASTARD,H.SAITO,A.LEBIVIC,V.OLLENDORFF, REMARK 1 AUTH 2 S.MARCHETTO,D.BIRNBAUM,J.P.BORG REMARK 1 TITL THE ERBB2/HER2 RECEPTOR DIFFERENTIALLY INTERACTS REMARK 1 TITL 2 WITH ERBIN AND PICK1 PSD-95/DLG/ZO-1 DOMAIN REMARK 1 TITL 3 PROTEINS REMARK 1 REF J.BIOL.CHEM. V. 276 15256 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M010032200 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.128 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.128 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1240 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 24313 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.128 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.128 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1235 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 22949 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 824 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 134 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 929.08 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 766.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 8 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8637 REMARK 3 NUMBER OF RESTRAINTS : 10570 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.085 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.077 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.084 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.103 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE REMARK 3 R (NO CUTOFF) BY 2.6% WATER MOLECULES 131, 132 AND 133 OCCUPY REMARK 3 THE SITE WHERE THE DISORDERED COMPONENT OF HIS1347 WITH REMARK 3 ALTERNATE CONFORMER B IS MODELED. REMARK 4 REMARK 4 1MFG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-02. REMARK 100 THE RCSB ID CODE IS RCSB016871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97861 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : DUAL SLITS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24313 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE V. 2.01 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-15%PEG 4000, 100MM AMMONIUM REMARK 280 ACETATE, 100MM SODIUM ACETATE, 10% GLYCEROL, PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 28.70850 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 300 REMARK: COORDINATES REPRESENT THE COMPLETE BIOLOGICAL ASSEMBLY 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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: 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 A1302 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A1307 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A1317 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A1317 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A1340 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ASN A1359 O - C - N ANGL. DEV. = -10.3 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 ASP A1288 46.11 -145.11 REMARK 500 LYS A1326 -4.30 68.79 REMARK 500 ASN A1359 -123.21 57.52 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 A 107 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH A 112 DISTANCE = 5.12 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MFL RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH THE PEPTIDE PHOSPHORYLATED AT REMARK 900 TYROSINE 1248 AND CRYSTALLIZED IN DIFFERENT FORM DBREF 1MFG A 1277 1371 UNP Q96RT1 LAP2_HUMAN 1277 1371 DBREF 1MFG B 1247 1255 PDB 1MFG 1MFG 1247 1255 SEQADV 1MFG GLY A 1277 UNP Q96RT1 ALA 1277 CLONING ARTIFACT SEQADV 1MFG SER A 1278 UNP Q96RT1 LYS 1278 CLONING ARTIFACT SEQADV 1MFG MET A 1279 UNP Q96RT1 GLY 1279 CLONING ARTIFACT SEQRES 1 A 95 GLY SER MET GLU ILE ARG VAL ARG VAL GLU LYS ASP PRO SEQRES 2 A 95 GLU LEU GLY PHE SER ILE SER GLY GLY VAL GLY GLY ARG SEQRES 3 A 95 GLY ASN PRO PHE ARG PRO ASP ASP ASP GLY ILE PHE VAL SEQRES 4 A 95 THR ARG VAL GLN PRO GLU GLY PRO ALA SER LYS LEU LEU SEQRES 5 A 95 GLN PRO GLY ASP LYS ILE ILE GLN ALA ASN GLY TYR SER SEQRES 6 A 95 PHE ILE ASN ILE GLU HIS GLY GLN ALA VAL SER LEU LEU SEQRES 7 A 95 LYS THR PHE GLN ASN THR VAL GLU LEU ILE ILE VAL ARG SEQRES 8 A 95 GLU VAL SER SER SEQRES 1 B 9 GLU TYR LEU GLY LEU ASP VAL PRO VAL FORMUL 3 HOH *134(H2 O) HELIX 1 1 GLU A 1346 PHE A 1357 1 12 SHEET 1 A 6 SER A1278 GLU A1286 0 SHEET 2 A 6 THR A1360 GLU A1368 -1 O LEU A1363 N VAL A1283 SHEET 3 A 6 LYS A1333 ALA A1337 -1 N LYS A1333 O VAL A1366 SHEET 4 A 6 ILE A1313 VAL A1318 -1 N ILE A1313 O ILE A1334 SHEET 5 A 6 PHE A1293 GLY A1297 -1 N SER A1296 O PHE A1314 SHEET 6 A 6 VAL B1253 PRO B1254 -1 O VAL B1253 N ILE A1295 SHEET 1 B 4 SER A1278 GLU A1286 0 SHEET 2 B 4 THR A1360 GLU A1368 -1 O LEU A1363 N VAL A1283 SHEET 3 B 4 LYS A1333 ALA A1337 -1 N LYS A1333 O VAL A1366 SHEET 4 B 4 TYR A1340 SER A1341 -1 O TYR A1340 N ALA A1337 CISPEP 1 ASP A 1288 PRO A 1289 0 0.38 CRYST1 26.605 57.417 30.439 90.00 100.59 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 0.037587 0.000000 0.007027 0.00000 SCALE2 0.000000 0.017416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.033422 0.00000 MASTER 275 0 0 1 10 0 0 6 0 0 0 9 END