PDB Short entry for 1WCP HEADER SIGNAL TRANSDUCTION 15-NOV-04 1WCP TITLE THEORETICAL MODEL OF THE FULL-LENGTH HUMAN P52 SHC ADAPTOR TITLE 2 PROTEIN OBTAINED BY HOMOLOGY MODELING AND 2 NS MOLECULAR TITLE 3 DYNAMICS SIMULATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHC TRANSFORMING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: P52 SHC, SH2 DOMAIN PROTEIN C1, SRC HOMOLOGY 2 COMPND 5 DOMAIN CONTAINING TRANSFORMING PROTEIN C1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS KEYWDS SIGNAL TRANSDUCTION, SRC HOMOLOGY AND COLLAGEN DOMAIN KEYWDS 2 PROTEIN, TYROSINE PHOSPHORYLATION, ALTERNATIVE PROMOTER KEYWDS 3 USAGE, GROWTH REGULATION, MULTIGENE FAMILY, SH2 DOMAIN EXPDTA THEORETICAL MODEL AUTHOR A.SUENAGA,A.KIYATKIN,M.HATAKEYAMA,M.TAIJI,J.HOEK,A.KONAGAYA, AUTHOR 2 B.KHOLODENKO REVDAT 1 29-SEP-05 1WCP 0 JRNL AUTH A.SUENAGA,A.KIYATKIN,M.HATAKEYAMA,N.FUTATSUGI, JRNL AUTH 2 N.OKIMOTO,Y.HIRANO,T.NARUMI,A.KAWAI,R.SUSUKITA, JRNL AUTH 3 T.KOISHI,H.FURUSAWA,K.YASUOKA,N.TAKADA,Y.OHNO, JRNL AUTH 4 M.TAIJI,T.EBISUZAKI,J.HOEK,A.KONAGAYA,B.KHOLODENKO JRNL TITL TYR317 PHOSPHORYLATION INCREASES SHC STRUCTURAL JRNL TITL 2 RIGIDITY AND REDUCES COUPLING OF DOMAIN MOTIONS JRNL TITL 3 REMOTE FROM THE PHOSPHORYLATION SITE AS REVEALED JRNL TITL 4 BY MOLECULAR DYNAMICS SIMULATIONS JRNL REF J.BIOL.CHEM. V. 279 4657 2004 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 1WCP COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 22-NOV-2004. REMARK 100 THE EBI ID CODE IS EBI-21684. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THE THREE DIMENSIONAL STRUCTURE OF FULL-LENGTH P52 SHC REMARK 220 WAS MODELED USING TWO EXPERIMENTALLY DETERMINED REMARK 220 STRUCTURES OF PTB AND SH2 DOMAINS OF SHC AS TEMPLATES REMARK 220 (PDB ACCESSION CODES 1SHC AND 1TCE RESPECTIVELY). WE REMARK 220 MAPPED THE TARGET SEQUENCE OF P52 SHC ONTO THOSE REMARK 220 MODELING TEMPLATES USING INTEGRATED SEQUENCE ALIGNMENT REMARK 220 TOOLS AND STRUCTURAL SUPERPOSITION ALGORITHMS OF THE REMARK 220 DEEPVIEW (SWISS-PDB VIEWER) PROGRAM. THEN THE INITIAL REMARK 220 SEQUENCE ALIGNMENT WAS OPTIMIZED MANUALLY AND SUBMITTED REMARK 220 TO THE SWISS-MODEL SERVER FOR MODEL BUILDING. THE REMARK 220 RESULTING PROTEIN MODEL (RESIDUES 17-474) WAS FURTHER REMARK 220 IMPROVED BY PERFORMING A 5000-STEP ENERGY MINIMIZATION REMARK 220 IN VACUUM USING MOE (MOLECULAR OPERATING ENVIRONMENT, REMARK 220 CHEMICAL COMPUTING GROUP INC.) PROGRAM. AFTER THE ENERGY REMARK 220 -MINIMIZATION FOR STRUCTURAL ADJUSTMENT, THE BACKBONE REMARK 220 ATOMS OF THE MODELED STRUCTURE OF FULL-LENGTH REMARK 220 UNPHOSPHORYLATED SHC, WAS PLACED AT A CENTER OF A SPHERE REMARK 220 OF TIP3P WATER MOLECULES (TOTAL NUMBER OF ATOMS 133,393) REMARK 220 . THE SIZE OF EACH SPHERE WAS CHOSEN SO THAT THE REMARK 220 DISTANCE OF THE ATOMS IN THE PROTEIN FROM THE WALL WAS REMARK 220 GREATER THAN 15.0 A. THE FULLY SOLVATED SYSTEM WAS REMARK 220 ENERGY- MINIMIZED USING 100 STEPS OF STEEPEST DESCENT REMARK 220 FOLLOWED BY 4900 STEPS OF CONJUGATE GRADIENT METHOD. ALL REMARK 220 MOLECULAR DYNAMICS (MD) SIMULATIONS WERE CARRIED OUT REMARK 220 USING THE MODIFIED AMBER 6.0 FOR MDM ON A PERSONAL REMARK 220 COMPUTER (ATHLON 1.6 GHZ) EQUIPPED WITH TWO MDGRAPE-2 REMARK 220 BOARDS (32 CHIPS; 512 GFLOPS), WHICH IS THE MAIN REMARK 220 COMPONENT OF THE MDM. A PARM 96 FORCE FIELD WAS ADOPTED REMARK 220 AND THE TIME STEP WAS SET AT 1 FS. ALL NON-COVALENT REMARK 220 INTERACTIONS, VAN DER WAALS AND COULOMB FORCES AND REMARK 220 ENERGIES, WERE CALCULATED USING THE MDM. THE BOND REMARK 220 LENGTHS INVOLVING HYDROGEN ATOMS WERE CONSTRAINED TO REMARK 220 EQUILIBRIUM LENGTH BY THE SHAKE METHOD. THE TEMPERATURE REMARK 220 OF THE SYSTEM WAS GRADUALLY HEATED TO 300 K DURING THE REMARK 220 FIRST 100 PS PERIOD. THEN THE TEMPERATURE WAS KEPT REMARK 220 CONSTANT BY COUPLING TO A TEMPERATURE BATH AT 300 K WITH REMARK 220 A COUPLING CONSTANT OF 2 PS. FOR EQUILIBRATING THE REMARK 220 SYSTEM OF UNPHOSPHORYLATED SHC, AN ADDITIONAL 900-PS MD REMARK 220 SIMULATION WAS PERFORMED AT 300 K (TOTAL OF 1 NS MD REMARK 220 SIMULATION FOR THE EQUILIBRATION). REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 400 REMARK 400 COMPOUND REMARK 400 SIGNALING ADAPTER THAT COUPLES ACTIVATED GROWTH FACTOR REMARK 400 RECEPTORS TO SIGNALING PATHWAY REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O PRO A 219 N HIS A 221 2.12 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 269 N - CA - C ANGL. DEV. = 18.3 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 TRP A 8 -35.57 70.31 REMARK 500 VAL A 15 -97.20 75.17 REMARK 500 ARG A 83 122.72 77.09 REMARK 500 ALA A 210 -92.32 82.33 REMARK 500 VAL A 344 -7.52 118.05 REMARK 500 VAL A 415 -160.60 129.07 REMARK 500 LEU A 438 73.54 134.21 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 29 MET A 30 133.02 REMARK 500 THR A 80 ARG A 81 -148.69 REMARK 500 LEU A 94 GLY A 95 147.38 REMARK 500 PRO A 269 VAL A 270 -147.51 REMARK 500 ASP A 420 HIS A 421 -149.66 REMARK 500 HIS A 421 ARG A 422 148.43 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MIL RELATED DB: PDB REMARK 900 TRANSFORMING PROTEIN REMARK 900 RELATED ID: 1N3H RELATED DB: PDB REMARK 900 COUPLING OF FOLDING AND BINDING IN THE PTB REMARK 900 DOMAIN OF THE SIGNALING PROTEIN SHC REMARK 900 RELATED ID: 1OY2 RELATED DB: PDB REMARK 900 COUPLING OF FOLDING AND BINDING IN THE PTB REMARK 900 DOMAIN OF THE SIGNALING PROTEIN SHC REMARK 900 RELATED ID: 1QG1 RELATED DB: PDB REMARK 900 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 REMARK 900 DOMAIN COMPLEXED WITH AN SHC-DERIVED PEPTIDE DBREF 1WCP A 1 457 UNP P29353 SHC1_HUMAN 1 457 SEQRES 1 A 457 GLY GLN LEU GLY GLY GLU GLU TRP THR ARG HIS GLY SER SEQRES 2 A 457 PHE VAL ASN LYS PRO THR ARG GLY TRP LEU HIS PRO ASN SEQRES 3 A 457 ASP LYS VAL MET GLY PRO GLY VAL SER TYR LEU VAL ARG SEQRES 4 A 457 TYR MET GLY CYS VAL GLU VAL LEU GLN SER MET ARG ALA SEQRES 5 A 457 LEU ASP PHE ASN THR ARG THR GLN VAL THR ARG GLU ALA SEQRES 6 A 457 ILE SER LEU VAL CYS GLU ALA VAL PRO GLY ALA LYS GLY SEQRES 7 A 457 ALA THR ARG ARG ARG LYS PRO CYS SER ARG PRO LEU SER SEQRES 8 A 457 SER ILE LEU GLY ARG SER ASN LEU LYS PHE ALA GLY MET SEQRES 9 A 457 PRO ILE THR LEU THR VAL SER THR SER SER LEU ASN LEU SEQRES 10 A 457 MET ALA ALA ASP CYS LYS GLN ILE ILE ALA ASN HIS HIS SEQRES 11 A 457 MET GLN SER ILE SER PHE ALA SER GLY GLY ASP PRO ASP SEQRES 12 A 457 THR ALA GLU TYR VAL ALA TYR VAL ALA LYS ASP PRO VAL SEQRES 13 A 457 ASN GLN ARG ALA CYS HIS ILE LEU GLU CYS PRO GLU GLY SEQRES 14 A 457 LEU ALA GLN ASP VAL ILE SER THR ILE GLY GLN ALA PHE SEQRES 15 A 457 GLU LEU ARG PHE LYS GLN TYR LEU ARG ASN PRO PRO LYS SEQRES 16 A 457 LEU VAL THR PRO HIS ASP ARG MET ALA GLY PHE ASP GLY SEQRES 17 A 457 SER ALA TRP ASP GLU GLU GLU GLU GLU PRO PRO ASP HIS SEQRES 18 A 457 GLN TYR TYR ASN ASP PHE PRO GLY LYS GLU PRO PRO LEU SEQRES 19 A 457 GLY GLY VAL VAL ASP MET ARG LEU ARG GLU GLY ALA ALA SEQRES 20 A 457 PRO GLY ALA ALA ARG PRO THR ALA PRO ASN ALA GLN THR SEQRES 21 A 457 PRO SER HIS LEU GLY ALA THR LEU PRO VAL GLY GLN PRO SEQRES 22 A 457 VAL GLY GLY ASP PRO GLU VAL ARG LYS GLN MET PRO PRO SEQRES 23 A 457 PRO PRO PRO CYS PRO GLY ARG GLU LEU PHE ASP ASP PRO SEQRES 24 A 457 SER TYR VAL ASN VAL GLN ASN LEU ASP LYS ALA ARG GLN SEQRES 25 A 457 ALA VAL GLY GLY ALA GLY PRO PRO ASN PRO ALA ILE ASN SEQRES 26 A 457 GLY SER ALA PRO ARG ASP LEU PHE ASP MET LYS PRO PHE SEQRES 27 A 457 GLU ASP ALA LEU ARG VAL PRO PRO PRO PRO GLN SER VAL SEQRES 28 A 457 SER MET ALA GLU GLN LEU ARG GLY GLU PRO TRP PHE HIS SEQRES 29 A 457 GLY LYS LEU SER ARG ARG GLU ALA GLU ALA LEU LEU GLN SEQRES 30 A 457 LEU ASN GLY ASP PHE LEU VAL ARG GLU SER THR THR THR SEQRES 31 A 457 PRO GLY GLN TYR VAL LEU THR GLY LEU GLN SER GLY GLN SEQRES 32 A 457 PRO LYS HIS LEU LEU LEU VAL ASP PRO GLU GLY VAL VAL SEQRES 33 A 457 ARG THR LYS ASP HIS ARG PHE GLU SER VAL SER HIS LEU SEQRES 34 A 457 ILE SER TYR HIS MET ASP ASN HIS LEU PRO ILE ILE SER SEQRES 35 A 457 ALA GLY SER GLU LEU CYS LEU GLN GLN PRO VAL GLU ARG SEQRES 36 A 457 LYS LEU HELIX 1 1 LEU A 23 VAL A 29 1 7 HELIX 2 2 PHE A 55 VAL A 73 1 19 HELIX 3 3 ALA A 171 LEU A 184 1 14 HELIX 4 4 ARG A 191 ARG A 202 1 12 HELIX 5 5 PRO A 218 GLN A 222 5 5 HELIX 6 6 ASP A 226 GLU A 231 1 6 HELIX 7 7 ALA A 246 ALA A 250 5 5 HELIX 8 8 PRO A 253 THR A 260 1 8 HELIX 9 9 ASN A 303 ASP A 308 5 6 HELIX 10 10 PRO A 320 GLY A 326 1 7 HELIX 11 11 SER A 368 LEU A 376 1 9 HELIX 12 12 VAL A 426 TYR A 432 1 7 SHEET 1 AA 4 GLY A 95 SER A 97 0 SHEET 2 AA 4 VAL A 34 VAL A 46 -1 O GLU A 45 N ARG A 96 SHEET 3 AA 4 MET A 104 SER A 111 -1 O MET A 104 N TYR A 40 SHEET 4 AA 4 SER A 114 LEU A 117 -1 O SER A 114 N SER A 111 SHEET 1 AB 5 GLY A 95 SER A 97 0 SHEET 2 AB 5 VAL A 34 VAL A 46 -1 O GLU A 45 N ARG A 96 SHEET 3 AB 5 ALA A 160 GLU A 165 -1 O CYS A 161 N VAL A 44 SHEET 4 AB 5 VAL A 148 ALA A 152 -1 O VAL A 148 N LEU A 164 SHEET 5 AB 5 PHE A 136 SER A 138 -1 O PHE A 136 N VAL A 151 SHEET 1 AC 5 ARG A 293 GLU A 294 0 SHEET 2 AC 5 GLN A 403 LEU A 409 -1 O LEU A 408 N ARG A 293 SHEET 3 AC 5 TYR A 394 GLN A 400 -1 O TYR A 394 N LEU A 409 SHEET 4 AC 5 ASP A 381 ARG A 385 -1 O ASP A 381 N LEU A 399 SHEET 5 AC 5 PHE A 363 GLY A 365 1 N HIS A 364 O VAL A 384 SHEET 1 AD 5 ARG A 293 GLU A 294 0 SHEET 2 AD 5 GLN A 403 LEU A 409 -1 O LEU A 408 N ARG A 293 SHEET 3 AD 5 TYR A 394 GLN A 400 -1 O TYR A 394 N LEU A 409 SHEET 4 AD 5 ASP A 381 ARG A 385 -1 O ASP A 381 N LEU A 399 SHEET 5 AD 5 GLN A 451 PRO A 452 1 O GLN A 451 N PHE A 382 CISPEP 1 GLU A 217 PRO A 218 0 4.84 CISPEP 2 PRO A 345 PRO A 346 0 -0.74 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000