PDB Short entry for 1MFG HEADER SIGNALING PROTEIN 10-AUG-02 1MFG TITLE THE STRUCTURE OF ERBIN PDZ DOMAIN BOUND TO THE CARBOXY-TERMINAL TAIL TITLE 2 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., SIGNALING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.BIRRANE,J.CHUNG,J.A.LADIAS REVDAT 4 14-FEB-24 1MFG 1 SEQADV 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 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,B.MARGOLIS, REMARK 1 AUTH 3 D.BIRNBAUM REMARK 1 TITL BIN: A BASOLATERAL PDZ PROTEIN THAT INTERACTS WITH THE REMARK 1 TITL 2 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 DELTA-CATENIN AND REMARK 1 TITL 3 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 MEMBRANES REMARK 1 TITL 2 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,S.MARCHETTO, REMARK 1 AUTH 2 D.BIRNBAUM,J.P.BORG REMARK 1 TITL THE ERBB2/HER2 RECEPTOR DIFFERENTIALLY INTERACTS WITH ERBIN REMARK 1 TITL 2 AND PICK1 PSD-95/DLG/ZO-1 DOMAIN 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 : 796 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: REMARK 3 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.6% REMARK 3 WATER MOLECULES 131, 132 AND 133 OCCUPY THE SITE WHERE REMARK 3 THE DISORDERED COMPONENT OF HIS1347 WITH ALTERNATE REMARK 3 CONFORMER B IS MODELED. REMARK 4 REMARK 4 1MFG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016871. 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 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. = 5.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MFL RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH THE PEPTIDE PHOSPHORYLATED AT TYROSINE REMARK 900 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