HEADER SIGNALING PROTEIN 22-FEB-10 2X72 TITLE CRYSTAL STRUCTURE OF THE CONSTITUTIVELY ACTIVE E113Q,D2C,D282C TITLE 2 RHODOPSIN MUTANT WITH BOUND GALPHACT PEPTIDE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RESIDUES 340-350; COMPND 10 SYNONYM: GACT PEPTIDE, TRANSDUCIN ALPHA-1 CHAIN; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: EYE; SOURCE 6 TISSUE: RETINA; SOURCE 7 CELL: ROD PHOTORECEPTOR; SOURCE 8 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 9 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM_CELL_LINE: HEK293S GNTI- CELLS; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 15 ORGANISM_COMMON: CATTLE; SOURCE 16 ORGANISM_TAXID: 9913 KEYWDS SIGNALING PROTEIN, CHROMOPHORE, LIPOPROTEIN, GLYCOPROTEIN, KEYWDS 2 TRANSMEMBRANE, RETINAL PROTEIN, G-PROTEIN COUPLED RECEPTOR, SENSORY KEYWDS 3 TRANSDUCTION, PHOTORECEPTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.STANDFUSS,P.C.EDWARDS,A.DANTONA,M.FRANSEN,G.XIE,D.D.OPRIAN, AUTHOR 2 G.F.X.SCHERTLER REVDAT 5 13-NOV-24 2X72 1 REMARK REVDAT 4 20-DEC-23 2X72 1 HETSYN LINK REVDAT 3 29-JUL-20 2X72 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 06-APR-11 2X72 1 JRNL REVDAT 1 16-MAR-11 2X72 0 JRNL AUTH J.STANDFUSS,P.C.EDWARDS,A.DANTONA,M.FRANSEN,G.XIE, JRNL AUTH 2 D.D.OPRIAN,G.F.X.SCHERTLER JRNL TITL THE STRUCTURAL BASIS OF AGONIST INDUCED ACTIVATION IN JRNL TITL 2 CONSTITUTIVELY ACTIVE RHODOPSIN JRNL REF NATURE V. 471 656 2011 JRNL REFN ISSN 0028-0836 JRNL PMID 21389983 JRNL DOI 10.1038/NATURE09795 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.STANDFUSS,G.XIE,P.C.EDWARDS,M.BURGHAMMER,D.D.OPRIAN, REMARK 1 AUTH 2 G.F.X.SCHERTLER REMARK 1 TITL CRYSTAL STRUCTURE OF A THERMALLY STABLE RHODOPSIN MUTANT. REMARK 1 REF J.MOL.BIOL. V. 372 1179 2007 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 17825322 REMARK 1 DOI 10.1016/J.JMB.2007.03.007 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 22912 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1158 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.9434 - 5.9941 0.98 3017 137 0.2212 0.2528 REMARK 3 2 5.9941 - 4.7602 1.00 2928 188 0.1877 0.2384 REMARK 3 3 4.7602 - 4.1592 1.00 2957 145 0.1668 0.1943 REMARK 3 4 4.1592 - 3.7792 0.99 2929 167 0.1754 0.2091 REMARK 3 5 3.7792 - 3.5085 0.99 2931 154 0.2125 0.2239 REMARK 3 6 3.5085 - 3.3018 0.98 2865 142 0.2472 0.2892 REMARK 3 7 3.3018 - 3.1365 0.75 2224 129 0.2745 0.2928 REMARK 3 8 3.1365 - 3.0000 0.65 1903 96 0.3146 0.3336 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.28 REMARK 3 B_SOL : 40.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -20.36350 REMARK 3 B22 (A**2) : -20.36350 REMARK 3 B33 (A**2) : 40.72690 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 3003 REMARK 3 ANGLE : 1.520 4058 REMARK 3 CHIRALITY : 0.082 453 REMARK 3 PLANARITY : 0.005 480 REMARK 3 DIHEDRAL : 21.715 1135 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2X72 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1290041995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25221 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3DQB AND 1GZM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 81.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.0-3.4 M AMMONIUM SULFATE, 100 MM REMARK 280 SODIUM ACETATE PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 121.99300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 70.43269 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 36.38533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 121.99300 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 70.43269 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 36.38533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 121.99300 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 70.43269 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 36.38533 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 121.99300 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 70.43269 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 36.38533 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 121.99300 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 70.43269 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 36.38533 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 121.99300 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 70.43269 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 36.38533 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 140.86538 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 72.77067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 140.86538 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 72.77067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 140.86538 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 72.77067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 140.86538 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 72.77067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 140.86538 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 72.77067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 140.86538 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 72.77067 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: 15700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.15600 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 2 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 113 TO GLN REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASP 282 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, LYS 341 TO LEU 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 PRO A 327 REMARK 465 LEU A 328 REMARK 465 GLY A 329 REMARK 465 ASP A 330 REMARK 465 ASP A 331 REMARK 465 GLU A 332 REMARK 465 ALA A 333 REMARK 465 SER A 334 REMARK 465 THR A 335 REMARK 465 THR A 336 REMARK 465 VAL A 337 REMARK 465 SER A 338 REMARK 465 LYS A 339 REMARK 465 THR A 340 REMARK 465 GLU A 341 REMARK 465 THR A 342 REMARK 465 SER A 343 REMARK 465 GLN A 344 REMARK 465 VAL A 345 REMARK 465 ALA A 346 REMARK 465 PRO A 347 REMARK 465 ALA A 348 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 MET A 1 C - N - CA ANGL. DEV. = 21.2 DEGREES REMARK 500 ALA A 272 CB - CA - C ANGL. DEV. = -10.9 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 SER A 22 129.41 -39.75 REMARK 500 GLN A 28 44.69 -99.28 REMARK 500 GLU A 33 158.69 -49.83 REMARK 500 VAL A 104 -8.77 -57.94 REMARK 500 LYS A 141 62.14 39.72 REMARK 500 CYS A 167 -21.09 -141.20 REMARK 500 SER A 176 -167.82 59.36 REMARK 500 HIS A 195 74.55 -109.86 REMARK 500 ASN A 199 37.81 74.70 REMARK 500 PHE A 212 -64.38 -130.50 REMARK 500 GLN A 237 65.23 -157.05 REMARK 500 ILE A 307 -60.15 -125.68 REMARK 500 CYS A 322 36.98 -93.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL REMARK 600 HEXADECANOATE (LPP): PARTIALLY DISORDERED REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): PART OF THE N-GLYCAN REMARK 600 DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE (PEF): PART OF REMARK 600 THE N-GLYCAN REMARK 600 PALMITIC ACID (PLM): PALMITOYLATION OF CYSTEINS REMARK 600 ALPHA-D-MANNOSE (MAN): PART OF N-GLYCAN REMARK 600 BETA-D-MANNOSE (BMA): PART OF N-GLYCAN REMARK 600 ACETYL GROUP (ACE): ACETYLATION OF N-TERMINUS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 LPP A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OV0 RELATED DB: PDB REMARK 900 CALCULATED 3D MODEL OF META-II RHODOPSIN BASED ON LIMITEDDATA OF REMARK 900 SITE-DIRECTED SPIN-LABELING REMARK 900 RELATED ID: 1AQG RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE RHODOPSIN-BOUND C-TERMINAL PEPTIDE OF THE REMARK 900 TRANSDUCIN ALPHA-SUBUNIT, 20 STRUCTURES REMARK 900 RELATED ID: 1N3M RELATED DB: PDB REMARK 900 THEORETICAL MODEL OF RHODOPSIN OLIGOMER REMARK 900 RELATED ID: 2I37 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PHOTOACTIVATED RHODOPSIN REMARK 900 RELATED ID: 1BOK RELATED DB: PDB REMARK 900 BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL , THEORETICAL REMARK 900 MODEL REMARK 900 RELATED ID: 2I36 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TRIGONAL CRYSTAL FORM OF GROUND- STATERHODOPSIN REMARK 900 RELATED ID: 1LVZ RELATED DB: PDB REMARK 900 METARHODOPSIN II BOUND STRUCTURE OF C-TERMINAL PEPTIDE OFALPHA- REMARK 900 SUBUNIT OF TRANSDUCIN REMARK 900 RELATED ID: 1TAG RELATED DB: PDB REMARK 900 TRANSDUCIN-ALPHA COMPLEXED WITH GDP AND MAGNESIUM (GT- ALPHA-GDP, T- REMARK 900 ALPHA-GDP) REMARK 900 RELATED ID: 1EDX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF AMINO TERMINUS OF BOVINE RHODOPSIN (RESIDUES REMARK 900 1- 40) REMARK 900 RELATED ID: 2J4Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A RHODOPSIN STABILIZING MUTANT EXPRESSED IN REMARK 900 MAMMALIAN CELLS REMARK 900 RELATED ID: 1FQK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HETERODIMERIC COMPLEX OF THE RGSDOMAIN OF REMARK 900 RGS9, AND THE GT/I1 CHIMERA ALPHA SUBUNIT [(RGS9)-(GT/I1ALPHA)-(GDP) REMARK 900 -(ALF4-)-(MG2+)] REMARK 900 RELATED ID: 1TND RELATED DB: PDB REMARK 900 TRANSDUCIN (ALPHA SUBUNIT) COMPLEXED WITH THE NONHYDROLYZABLE GTP REMARK 900 ANALOGUE GTP GAMMA S REMARK 900 RELATED ID: 1VQX RELATED DB: PDB REMARK 900 ARRESTIN-BOUND NMR STRUCTURES OF THE PHOSPHORYLATED CARBOXY- REMARK 900 TERMINAL DOMAIN OF RHODOPSIN, REFINED REMARK 900 RELATED ID: 1LN6 RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN (METARHODOPSIN II) REMARK 900 RELATED ID: 1JFP RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN (DARK ADAPTED) REMARK 900 RELATED ID: 1OV1 RELATED DB: PDB REMARK 900 CALCULATED 3D MODEL OF AN ACTIVATED "STRAITJACKED" RHODOPSIN REMARK 900 RELATED ID: 1F88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN REMARK 900 RELATED ID: 1BOJ RELATED DB: PDB REMARK 900 BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH ALL-TRANS RETINAL, REMARK 900 METARHODOPSIN II MODEL, THEORETICAL MODEL REMARK 900 RELATED ID: 1EDS RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF INTRADISKAL LOOP 1 OF BOVINE RHODOPSIN REMARK 900 (RHODOPSIN RESIDUES 92-123) REMARK 900 RELATED ID: 1NZS RELATED DB: PDB REMARK 900 NMR STRUCTURES OF PHOSPHORYLATED CARBOXY TERMINUS OF REMARK 900 BOVINERHODOPSIN IN ARRESTIN-BOUND STATE REMARK 900 RELATED ID: 1U19 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.2 ANGSTROMSRESOLUTION REMARK 900 RELATED ID: 1FQJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HETEROTRIMERIC COMPLEX OF THE RGSDOMAIN OF REMARK 900 RGS9, THE GAMMA SUBUNIT OF PHOSPHODIESTERASE ANDTHE GT/I1 CHIMERA REMARK 900 ALPHA SUBUNIT [( RGS9)-(PDEGAMMA)-(GT/I1ALPHA)-(GDP)-(ALF4-)-(MG2+)] REMARK 900 RELATED ID: 1TAD RELATED DB: PDB REMARK 900 TRANSDUCIN-ALPHA (GT-ALPHA-GDP-ALF, T-ALPHA-GDP-ALF ) COMPLEXED REMARK 900 WITH GDP AND ALUMINUM FLUORIDE REMARK 900 RELATED ID: 1FDF RELATED DB: PDB REMARK 900 HELIX 7 BOVINE RHODOPSIN REMARK 900 RELATED ID: 1EDW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THIRD INTRADISKAL LOOP OF BOVINE RHODOPSIN REMARK 900 (RESIDUES 268-293) REMARK 900 RELATED ID: 1HZX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN REMARK 900 RELATED ID: 1L9H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BOVINE RHODOPSIN AT 2.6 ANGSTROMSRESOLUTION REMARK 900 RELATED ID: 2I35 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RHOMBOHEDRAL CRYSTAL FORM OF GROUND -STATE REMARK 900 RHODOPSIN REMARK 900 RELATED ID: 1GZM RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE RHODOPSIN IN A TRIGONAL CRYSTAL FORM REMARK 900 RELATED ID: 1EDV RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF 2ND INTRADISKAL LOOP OF BOVINE RHODOPSIN REMARK 900 (RESIDUES 172-205) DBREF 2X72 A 0 0 PDB 2X72 2X72 0 0 DBREF 2X72 A 1 348 UNP P02699 OPSD_BOVIN 1 348 DBREF 2X72 B 340 350 UNP P04695 GNAT1_BOVIN 340 350 SEQADV 2X72 CYS A 2 UNP P02699 ASN 2 ENGINEERED MUTATION SEQADV 2X72 GLN A 113 UNP P02699 GLU 113 ENGINEERED MUTATION SEQADV 2X72 CYS A 282 UNP P02699 ASP 282 ENGINEERED MUTATION SEQADV 2X72 LEU B 341 UNP P04695 LYS 341 ENGINEERED MUTATION SEQRES 1 A 349 ACE MET CYS GLY THR GLU GLY PRO ASN PHE TYR VAL PRO SEQRES 2 A 349 PHE SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU SEQRES 3 A 349 ALA PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER SEQRES 4 A 349 MET LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY SEQRES 5 A 349 PHE PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN SEQRES 6 A 349 HIS LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU SEQRES 7 A 349 ASN LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY SEQRES 8 A 349 PHE THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE SEQRES 9 A 349 VAL PHE GLY PRO THR GLY CYS ASN LEU GLN GLY PHE PHE SEQRES 10 A 349 ALA THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL SEQRES 11 A 349 VAL LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO SEQRES 12 A 349 MET SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET SEQRES 13 A 349 GLY VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA SEQRES 14 A 349 ALA PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU SEQRES 15 A 349 GLY MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO SEQRES 16 A 349 HIS GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET SEQRES 17 A 349 PHE VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE SEQRES 18 A 349 PHE CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA SEQRES 19 A 349 ALA ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA SEQRES 20 A 349 GLU LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE SEQRES 21 A 349 ALA PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA SEQRES 22 A 349 PHE TYR ILE PHE THR HIS GLN GLY SER CYS PHE GLY PRO SEQRES 23 A 349 ILE PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER SEQRES 24 A 349 ALA VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS SEQRES 25 A 349 GLN PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY SEQRES 26 A 349 LYS ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SEQRES 27 A 349 SER LYS THR GLU THR SER GLN VAL ALA PRO ALA SEQRES 1 B 11 ILE LEU GLU ASN LEU LYS ASP CYS GLY LEU PHE MODRES 2X72 ASN A 15 ASN GLYCOSYLATION SITE HET ACE A 0 3 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET PEF A 401 47 HET BOG A 402 20 HET PLM A 403 17 HET PLM A 404 17 HET RET A 410 21 HET LPP A 411 37 HET ACT A 412 4 HETNAM ACE ACETYL GROUP HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETNAM PLM PALMITIC ACID HETNAM RET RETINAL HETNAM LPP 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HETNAM 2 LPP HEXADECANOATE HETNAM ACT ACETATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN PEF 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE HETSYN LPP 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE; L-B,G- HETSYN 2 LPP DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT; 3-SN- HETSYN 3 LPP PHOSPHATIDIC ACID; 1,2-DIPALMITOYLDISODIUM SALT FORMUL 1 ACE C2 H4 O FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 3 BMA C6 H12 O6 FORMUL 3 MAN 2(C6 H12 O6) FORMUL 4 PEF C37 H74 N O8 P FORMUL 5 BOG C14 H28 O6 FORMUL 6 PLM 2(C16 H32 O2) FORMUL 8 RET C20 H28 O FORMUL 9 LPP C35 H69 O8 P FORMUL 10 ACT C2 H3 O2 1- FORMUL 11 HOH *18(H2 O) HELIX 1 AA1 SER A 14 GLY A 18 5 5 HELIX 2 AA2 GLU A 33 HIS A 65 1 33 HELIX 3 AA3 LYS A 66 ARG A 69 5 4 HELIX 4 AA4 THR A 70 LEU A 72 5 3 HELIX 5 AA5 ASN A 73 GLY A 90 1 18 HELIX 6 AA6 GLY A 90 LEU A 99 1 10 HELIX 7 AA7 PHE A 105 LYS A 141 1 37 HELIX 8 AA8 GLY A 149 ALA A 169 1 21 HELIX 9 AA9 PRO A 170 GLY A 174 5 5 HELIX 10 AB1 ASN A 199 PHE A 212 1 14 HELIX 11 AB2 PHE A 212 GLN A 236 1 25 HELIX 12 AB3 SER A 240 THR A 277 1 38 HELIX 13 AB4 GLY A 284 THR A 297 1 14 HELIX 14 AB5 THR A 297 ILE A 307 1 11 HELIX 15 AB6 ASN A 310 CYS A 322 1 13 HELIX 16 AB7 LEU B 341 CYS B 347 1 7 SHEET 1 AA1 2 THR A 4 GLY A 6 0 SHEET 2 AA1 2 PHE A 9 VAL A 11 -1 O VAL A 11 N THR A 4 SHEET 1 AA2 2 TYR A 178 GLU A 181 0 SHEET 2 AA2 2 SER A 186 ILE A 189 -1 O SER A 186 N GLU A 181 SSBOND 1 CYS A 2 CYS A 282 1555 1555 2.05 SSBOND 2 CYS A 110 CYS A 187 1555 1555 2.06 LINK C ACE A 0 N MET A 1 1555 1555 1.35 LINK ND2 ASN A 15 C1 NAG C 1 1555 1555 1.43 LINK SG CYS A 322 C1 PLM A 404 1555 1555 1.67 LINK SG CYS A 323 C1 PLM A 403 1555 1555 1.69 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.45 LINK O6 BMA C 3 C1 MAN C 5 1555 1555 1.46 CRYST1 243.986 243.986 109.156 90.00 90.00 120.00 H 3 2 18 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 0.004099 0.002366 0.000000 0.00000 SCALE2 0.000000 0.004733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009161 0.00000 HETATM 1 C ACE A 0 57.108 -44.928 39.535 1.00107.97 C HETATM 2 O ACE A 0 56.877 -43.696 39.502 1.00 95.75 O HETATM 3 CH3 ACE A 0 58.499 -45.518 39.667 1.00 88.02 C