HEADER SIGNAL TRANSDUCTION PROTEIN 28-MAR-95 1SEM TITLE STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND TITLE 2 OF SEQUENCE SPECIFICITY IN SH3 DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEM-5; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE- COMPND 7 PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG); COMPND 8 CHAIN: C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: GRB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET19B; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 11 ORGANISM_TAXID: 10090 KEYWDS SRC-HOMOLOGY 3 (SH3) DOMAIN, PEPTIDE-BINDING PROTEIN, KEYWDS 2 GUANINE NUCLEOTIDE EXCHANGE FACTOR, SIGNAL TRANSDUCTION KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.A.LIM,F.M.RICHARDS,R.O.FOX REVDAT 2 24-FEB-09 1SEM 1 VERSN REVDAT 1 10-JUL-95 1SEM 0 JRNL AUTH W.A.LIM,F.M.RICHARDS,R.O.FOX JRNL TITL STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING JRNL TITL 2 ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 JRNL TITL 3 DOMAINS. JRNL REF NATURE V. 372 375 1994 JRNL REFN ISSN 0028-0836 JRNL PMID 7802869 JRNL DOI 10.1038/372375A0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.ROZAKIS-ADCOCK,R.FERNLEY,J.WADE,T.PAWSON, REMARK 1 AUTH 2 D.BOWTELL REMARK 1 TITL THE SH2 AND SH3 DOMAINS OF MAMMALIAN GRB2 COUPLE REMARK 1 TITL 2 THE EGF RECEPTOR TO THE RAS ACTIVATOR MSOS1 REMARK 1 REF NATURE V. 363 83 1993 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.G.CLARK,M.J.STERN,H.R.HORVITZ REMARK 1 TITL C. ELEGANS CELL-SIGNALLING GENE SEM-5 ENCODES A REMARK 1 TITL 2 PROTEIN WITH SH2 AND SH3 DOMAINS REMARK 1 REF NATURE V. 356 340 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1061 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 67 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.54 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SSBOND CRYSTALS GROWN IN THE REMARK 3 PRESENCE OF DTT; DISULFIDE BOND THOUGHT TO FORM AFTER INITIAL REMARK 3 EXPOSURE TO X-RAYS; CAUSED STABLE SHIFT IN UNIT CELL REMARK 3 DIMENSIONS. REMARK 4 REMARK 4 1SEM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6912 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08000 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 34.20500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 450 REMARK 450 SOURCE REMARK 450 REMARK 450 MOLECULE_NAME: MSOS, 10-RESIDUE PEPTIDE REMARK 450 (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG). PEPTIDE IS REMARK 450 FROM BIOLOGICAL SEQUENCE, BUT IS CHEMICALLY SYNTHESIZED. 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 GLU B 155 REMARK 465 ARG C 9 REMARK 465 ARG C 10 REMARK 465 ARG D 9 REMARK 465 ARG D 10 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 157 CG CD CE NZ 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 197 -120.01 55.93 REMARK 500 TYR A 211 -60.16 -138.49 REMARK 500 LYS B 186 40.78 -146.71 REMARK 500 ASN B 197 -116.53 67.48 REMARK 500 PRO C 6 153.34 -45.05 REMARK 500 PRO C 7 101.19 -42.97 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 36 DISTANCE = 5.71 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE D 1 DBREF 1SEM A 155 212 UNP P29355 SEM5_CAEEL 155 212 DBREF 1SEM B 155 212 UNP P29355 SEM5_CAEEL 155 212 DBREF 1SEM C 1 10 PDB 1SEM 1SEM 1 10 DBREF 1SEM D 1 10 PDB 1SEM 1SEM 1 10 SEQRES 1 A 58 GLU THR LYS PHE VAL GLN ALA LEU PHE ASP PHE ASN PRO SEQRES 2 A 58 GLN GLU SER GLY GLU LEU ALA PHE LYS ARG GLY ASP VAL SEQRES 3 A 58 ILE THR LEU ILE ASN LYS ASP ASP PRO ASN TRP TRP GLU SEQRES 4 A 58 GLY GLN LEU ASN ASN ARG ARG GLY ILE PHE PRO SER ASN SEQRES 5 A 58 TYR VAL CYS PRO TYR ASN SEQRES 1 B 58 GLU THR LYS PHE VAL GLN ALA LEU PHE ASP PHE ASN PRO SEQRES 2 B 58 GLN GLU SER GLY GLU LEU ALA PHE LYS ARG GLY ASP VAL SEQRES 3 B 58 ILE THR LEU ILE ASN LYS ASP ASP PRO ASN TRP TRP GLU SEQRES 4 B 58 GLY GLN LEU ASN ASN ARG ARG GLY ILE PHE PRO SER ASN SEQRES 5 B 58 TYR VAL CYS PRO TYR ASN SEQRES 1 C 10 ACE PRO PRO PRO VAL PRO PRO ARG ARG ARG SEQRES 1 D 10 ACE PRO PRO PRO VAL PRO PRO ARG ARG ARG HET ACE C 1 3 HET ACE D 1 3 HETNAM ACE ACETYL GROUP FORMUL 3 ACE 2(C2 H4 O) FORMUL 5 HOH *67(H2 O) HELIX 1 1 SER A 205 TYR A 207 5 3 HELIX 2 2 SER B 205 TYR B 207 5 3 SHEET 1 A 5 VAL A 208 ASN A 212 0 SHEET 2 A 5 PHE A 158 ALA A 161 -1 N GLN A 160 O CYS A 209 SHEET 3 A 5 VAL A 180 ASN A 185 -1 N ILE A 181 O VAL A 159 SHEET 4 A 5 TRP A 191 LEU A 196 -1 N GLN A 195 O THR A 182 SHEET 5 A 5 ARG A 199 PRO A 204 -1 N PHE A 203 O TRP A 192 SHEET 1 B 5 VAL B 208 PRO B 210 0 SHEET 2 B 5 PHE B 158 ALA B 161 -1 N GLN B 160 O CYS B 209 SHEET 3 B 5 VAL B 180 ASN B 185 -1 N ILE B 181 O VAL B 159 SHEET 4 B 5 TRP B 191 LEU B 196 -1 N GLN B 195 O THR B 182 SHEET 5 B 5 ARG B 199 PRO B 204 -1 N PHE B 203 O TRP B 192 SSBOND 1 CYS A 209 CYS B 209 1555 1555 2.03 LINK C ACE C 1 N PRO C 2 1555 1555 1.35 LINK C ACE D 1 N PRO D 2 1555 1555 1.35 SITE 1 AC2 1 HOH D 21 CRYST1 26.912 68.410 35.029 90.00 94.71 90.00 P 1 21 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 0.037158 0.000000 0.003061 0.00000 SCALE2 0.000000 0.014618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028645 0.00000