PDB Short entry for 2I93 HEADER 04-SEP-06 2I93 TITLE MODEL OF THE STRUCTURE OF THE START DOMAINS OF HUMAN TITLE 2 STEROIDOGENIC ACUTE REGULATORY PROTEIN (STAR) IN COMPLEX TITLE 3 WITH CHOLESTEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROIDOGENIC ACUTE REGULATORY PROTEIN (STAR); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: START DOMAIN (STARD1) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN KEYWDS STEROIDOGENIC ACUTE REGULATORY PROTEIN, STAR, STAR-RELATED KEYWDS 2 LIPID TRANSFER, START, MLN64, CHOLESTEROL, DOCKING, KEYWDS 3 HOMOLOGY MODELING, GENERALIZED-BORN, BINDING, MOLECULAR KEYWDS 4 DYNAMICS, CHOLESTEROL RELEASE EXPDTA THEORETICAL MODEL AUTHOR M.MURCIA,J.D.FARALDO-GOMEZ,F.R.MAXFIELD,ROUX B. REVDAT 3 05-DEC-06 2I93 1 JRNL REVDAT 2 24-OCT-06 2I93 1 JRNL REVDAT 1 19-SEP-06 2I93 0 JRNL AUTH M.MURCIA,J.D.FARALDO-GOMEX,F.R.MAXFIELD,B.ROUX JRNL TITL MODELING THE STRUCTURE OF THE START DOMAINS OF JRNL TITL 2 MLN64 AND STAR PROTEINS IN COMPLEX WITH JRNL TITL 3 CHOLESTEROL. JRNL REF J.LIPID RES. V. 47 2614 2006 JRNL REFN ASTM JLPRAW US ISSN 0022-2275 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM 31A0 REMARK 3 AUTHORS : BROOKS ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A HOMOLOGY MODEL OF THE THREE- REMARK 3 DIMENSIONAL STRUCTURE OF HUMAN STAR-START IN COMPLEX WITH REMARK 3 CHOLESTEROL WAS BUILT WITH CHARMM USING THE MLN64-START REMARK 3 CRYSTAL STRUCTURE AS A TEMPLATE (PDB ID : 1EM2), BASED ON A REMARK 3 PAIR-WISE SEQUENCE ALIGNMENT PRODUCED WITH CLUSTALW. THE REMARK 3 IDENTITY OF BOTH SEQUENCES IS 36%, WITH NO INSERTIONS OR REMARK 3 DELETIONS. THE COORDINATES OF ALL BACKBONE ATOMS AS WELL AS REMARK 3 THOSE OF CONSERVED OR STRUCTURALLY SIMILAR SIDE CHAINS (E.G. REMARK 3 ASP AND ASN) WERE PRESERVED FROM THE TEMPLATE. OTHERWISE, NEW REMARK 3 COORDINATES WERE ASSIGNED USING SCWRL 3.0, AND SUBSEQUENTLY REMARK 3 ENERGY-MINIMIZED. A CHOLESTEROL MOLECULE IN THE PREFERRED REMARK 3 BINDING MODE IN MLN64-START (SEE THE CORRESPONDING MODEIL) WAS REMARK 3 INCLUDED WHILE BUILDING THE MODEL. THE THREE-DIMENSIONAL MODEL REMARK 3 OF THE ATOMIC STRUCTURE OF STAR-START IN COMPLEX WITH REMARK 3 CHOLESTEROL WAS FINALLY ANALYZED THROUGH MD SIMULATIONS (10 REMARK 3 INDEPENDENT RUNS OF 1.5 NS EACH). ALL MD SIMULATIONS WERE REMARK 3 PERFORMED USING VERSION C31A0 OF THE CHARMM BIOMOLECULAR REMARK 3 SIMULATION SOFTWARE ALONGSIDE THE CHARMM22/CMAP ALL-ATOM REMARK 3 PROTEIN FORCE FIELD. AN IMPLICIT MODEL OF THE SOLVENT WAS USED REMARK 3 IN ALL SIMULATIONS, AS IMPLEMENTED IN THE GBSW MODULE OF REMARK 3 CHARMM. REMARK 4 REMARK 4 2I93 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY WAS DEPOSITED AT RCSB ON 04-SEP-2006. REMARK 100 THE RCSB ID CODE IS RCSB039291. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: 10 THEORETICAL MODELS TAKEN FROM THE 10 LAST REMARK 220 CONFIGURATIONS OF 10 INDEPENDENT MD SIMULATIONS OF 1.5 REMARK 220 NS EACH. THIS THEORETICAL MODEL ENTRY WAS NOT ANNOTATED REMARK 220 AND NOT VALIDATED BY THE WWPDB STAFF AND THEREFORE MAY REMARK 220 NOT CONFORM TO THE PDB FORMAT. 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EM2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APO FORM OF THE START DOMAIN OF REMARK 900 MLN64 REMARK 900 RELATED ID: 1JSS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APO FORM OF THE START DOMAIN OF REMARK 900 STARD4 REMARK 900 RELATED ID: 1LN1-3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF THE BOUND FORM OF THE START DOMAIN OF REMARK 900 PCTP IN COMPLEX WITH PC REMARK 900 RELATED ID: 1IMG RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF THE START DOMAIN OF STAR (HUMAN) REMARK 900 RELATED ID: 1ILJ RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF THE START DOMAIN OF STAR (HAMSTER) REMARK 900 RELATED ID: PENDING RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF THE START DOMAIN OF MLN64 (HUMAN) IN REMARK 900 COMPLEX WITH CHOLESTEROL (MURCIA ET AL.) THE CHOLESTEROL REMARK 900 ORIENTATION OF THIS MODEL IS USED AS A TEMPLATE WHEN REMARK 900 BUILDING STAR'S MODEL SEQRES 1 A 214 LEU TYR SER ASP GLN GLU LEU ALA TYR LEU GLN GLN GLY SEQRES 2 A 214 GLU GLU ALA MET GLN LYS ALA LEU GLY ILE LEU SER ASN SEQRES 3 A 214 GLN GLU GLY TRP LYS LYS GLU SER GLN GLN ASP ASN GLY SEQRES 4 A 214 ASP LYS VAL MET SER LYS VAL VAL PRO ASP VAL GLY LYS SEQRES 5 A 214 VAL PHE ARG LEU GLU VAL VAL VAL ASP GLN PRO MET GLU SEQRES 6 A 214 ARG LEU TYR GLU GLU LEU VAL GLU ARG MET GLU ALA MET SEQRES 7 A 214 GLY GLU TRP ASN PRO ASN VAL LYS GLU ILE LYS VAL LEU SEQRES 8 A 214 GLN LYS ILE GLY LYS ASP THR PHE ILE THR HIS GLU LEU SEQRES 9 A 214 ALA ALA GLU ALA ALA GLY ASN LEU VAL GLY PRO ARG ASP SEQRES 10 A 214 PHE VAL SER VAL ARG CYS ALA LYS ARG ARG GLY SER THR SEQRES 11 A 214 CYS VAL LEU ALA GLY MET ASP THR ASP PHE GLY ASN MET SEQRES 12 A 214 PRO GLU GLN LYS GLY VAL ILE ARG ALA GLU HIS GLY PRO SEQRES 13 A 214 THR CYS MET VAL LEU HIS PRO LEU ALA GLY SER PRO SER SEQRES 14 A 214 LYS THR LYS LEU THR TRP LEU LEU SER ILE ASP LEU LYS SEQRES 15 A 214 GLY TRP LEU PRO LYS SER ILE ILE ASN GLN VAL LEU SER SEQRES 16 A 214 GLN THR GLN VAL ASP PHE ALA ASN HIS LEU ARG LYS ARG SEQRES 17 A 214 LEU GLU SER HIS PRO ALA HET CLR A 1 74 HETNAM CLR CHOLESTEROL FORMUL 2 CLR C27 H46 O HELIX 1 1 SER A 69 SER A 91 1 23 HELIX 2 2 PRO A 129 GLU A 139 1 11 HELIX 3 3 GLU A 142 TRP A 147 5 6 HELIX 4 4 ALA A 231 SER A 233 5 3 HELIX 5 5 PRO A 252 HIS A 278 1 27 SHEET 1 A 9 LYS A 97 GLN A 101 0 SHEET 2 A 9 LYS A 107 VAL A 113 -1 O VAL A 108 N SER A 100 SHEET 3 A 9 GLY A 117 VAL A 126 -1 O VAL A 119 N LYS A 111 SHEET 4 A 9 THR A 237 LEU A 243 -1 O THR A 237 N VAL A 126 SHEET 5 A 9 THR A 223 PRO A 229 -1 N HIS A 228 O LYS A 238 SHEET 6 A 9 CYS A 197 ASP A 203 -1 N GLY A 201 O THR A 223 SHEET 7 A 9 ARG A 182 ARG A 192 -1 N VAL A 187 O MET A 202 SHEET 8 A 9 THR A 164 ALA A 171 -1 N GLU A 169 O PHE A 184 SHEET 9 A 9 VAL A 151 ILE A 160 -1 N LYS A 152 O LEU A 170 SHEET 1 B 8 LYS A 97 GLN A 101 0 SHEET 2 B 8 LYS A 107 VAL A 113 -1 O VAL A 108 N SER A 100 SHEET 3 B 8 GLY A 117 VAL A 126 -1 O VAL A 119 N LYS A 111 SHEET 4 B 8 THR A 237 LEU A 243 -1 O THR A 237 N VAL A 126 SHEET 5 B 8 THR A 223 PRO A 229 -1 N HIS A 228 O LYS A 238 SHEET 6 B 8 CYS A 197 ASP A 203 -1 N GLY A 201 O THR A 223 SHEET 7 B 8 ARG A 182 ARG A 192 -1 N VAL A 187 O MET A 202 SHEET 8 B 8 ILE A 216 ARG A 217 1 O ILE A 216 N ASP A 183 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