cmd.read_pdbstr("""\ HEADER RIBOSOME 19-OCT-05 2BCW \ TITLE COORDINATES OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11,C- \ TITLE 2 TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 AND A PORTION OF THE G' \ TITLE 3 DOMAIN OF ELONGATION FACTOR G, AS FITTED INTO CRYO-EM MAP OF AN \ TITLE 4 ESCHERICHIA COLI 70S*EF-G*GDP*FUSIDIC ACID COMPLEX \ COMPND MOL_ID: 1; \ COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L11; \ COMPND 3 CHAIN: A; \ COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; \ COMPND 5 MOL_ID: 2; \ COMPND 6 MOLECULE: 50S RIBOSOMAL PROTEIN L7/L12; \ COMPND 7 CHAIN: B; \ COMPND 8 FRAGMENT: C-TERMINAL DOMAIN; \ COMPND 9 SYNONYM: L8; \ COMPND 10 MOL_ID: 3; \ COMPND 11 MOLECULE: ELONGATION FACTOR G; \ COMPND 12 CHAIN: C; \ COMPND 13 FRAGMENT: A PORTION OF G' DOMAIN'; \ COMPND 14 SYNONYM: EF-G \ SOURCE MOL_ID: 1; \ SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; \ SOURCE 3 ORGANISM_TAXID: 2336; \ SOURCE 4 MOL_ID: 2; \ SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; \ SOURCE 6 ORGANISM_TAXID: 562; \ SOURCE 7 MOL_ID: 3; \ SOURCE 8 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; \ SOURCE 9 ORGANISM_TAXID: 274 \ KEYWDS COMPONENTS INVOLVED IN INTERACTION BETWEEN EF-G AND L7/L12 STALK BASE \ KEYWDS 2 OF THE RIBOSOME, RIBOSOME \ EXPDTA ELECTRON MICROSCOPY \ MDLTYP CA ATOMS ONLY, CHAIN A, B, C \ AUTHOR P.P.DATTA,M.R.SHARMA,L.QI,J.FRANK,R.K.AGRAWAL \ REVDAT 4 14-FEB-24 2BCW 1 REMARK \ REVDAT 3 18-JUL-18 2BCW 1 REMARK \ REVDAT 2 24-FEB-09 2BCW 1 VERSN \ REVDAT 1 20-DEC-05 2BCW 0 \ JRNL AUTH P.P.DATTA,M.R.SHARMA,L.QI,J.FRANK,R.K.AGRAWAL \ JRNL TITL INTERACTION OF THE G' DOMAIN OF ELONGATION FACTOR G AND THE \ JRNL TITL 2 C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 DURING \ JRNL TITL 3 TRANSLOCATION AS REVEALED BY CRYO-EM. \ JRNL REF MOL.CELL V. 20 723 2005 \ JRNL REFN ISSN 1097-2765 \ JRNL PMID 16337596 \ JRNL DOI 10.1016/J.MOLCEL.2005.10.028 \ REMARK 1 \ REMARK 1 REFERENCE 1 \ REMARK 1 AUTH B.T.WIMBERLY,R.GUYMON,J.P.MCCUTCHEON,S.W.WHITE, \ REMARK 1 AUTH 2 V.RAMAKRISHNAN \ REMARK 1 TITL A DETAILED VIEW OF A RIBOSOMAL ACTIVE SITE: THE STRUCTURE OF \ REMARK 1 TITL 2 THE L11-RNA COMPLEX \ REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 97 491 1999 \ REMARK 1 REFN ISSN 0092-8674 \ REMARK 1 PMID 10338213 \ REMARK 1 DOI 10.1016/S0092-8674(00)80759-X \ REMARK 1 REFERENCE 2 \ REMARK 1 AUTH M.LEIJONMARCK,A.LILJAS \ REMARK 1 TITL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN \ REMARK 1 TITL 2 L7/L12 FROM ESCHERICHIA COLI AT 1.7 \ REMARK 1 REF J.MOL.BIOL. V. 195 555 1987 \ REMARK 1 REFN ISSN 0022-2836 \ REMARK 1 PMID 3309338 \ REMARK 1 DOI 10.1016/0022-2836(87)90183-5 \ REMARK 1 REFERENCE 3 \ REMARK 1 AUTH A.AEVARSSON,E.BRAZHNIKOV,M.GARBER,J.ZHELTONOSOVA, \ REMARK 1 AUTH 2 Y.CHIRGADZE,S.AL-KARADAGHI,L.A.SVENSSON,A.LILJAS \ REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE RIBOSOMAL TRANSLOCASE: \ REMARK 1 TITL 2 ELONGATION FACTOR G FROM THERMUS THERMOPHILUS \ REMARK 1 REF EMBO J. V. 13 3669 1994 \ REMARK 1 REFN ISSN 0261-4189 \ REMARK 1 PMID 8070397 \ REMARK 2 \ REMARK 2 RESOLUTION. 11.20 ANGSTROMS. \ REMARK 3 \ REMARK 3 REFINEMENT. \ REMARK 3 SOFTWARE PACKAGES : OTHER, SPIDER \ REMARK 3 RECONSTRUCTION SCHEMA : NULL \ REMARK 3 \ REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT \ REMARK 3 PDB ENTRY : 1MMS \ REMARK 3 REFINEMENT SPACE : REAL \ REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT \ REMARK 3 REFINEMENT TARGET : THE X-RAY CRYSTALLOGRAPHIC \ REMARK 3 STRUCTURE OF THE EF-G INDIVIDUAL \ REMARK 3 DOMAINS WERE FITTED INTO THE CRYO- \ REMARK 3 EM MAP OF THE 70S*EF-G-UG*GDP* \ REMARK 3 FUSIDIC ACID COMPLEX USING O. THE \ REMARK 3 G' DOMAIN WITHIN DOMAIN I WAS \ REMARK 3 SEPARATELY FITTED, USING A \ REMARK 3 COMBINATION OF MANUAL RIGID-BODY \ REMARK 3 DOCKING AND FLEXIBLE DOCKING \ REMARK 3 APPROACHES, AND TAKING INTO \ REMARK 3 CONSIDERATION BOTH THE CRYO-EM \ REMARK 3 ENVELOPE AND THE POSITIONAL \ REMARK 3 CONSTRAINTS IMPOSED BY THE UG \ REMARK 3 DENSITY. X-RAY CRYSTALLOGRAPHIC \ REMARK 3 STRUCTURES OF THE N-TERMINAL \ REMARK 3 DOMAIN OF PROTEIN L11 AND C- \ REMARK 3 TERMINAL DOMAIN OF PROTEIN L7/L12 \ REMARK 3 WERE FITTED AS RIGID BODIES. \ REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL \ REMARK 3 \ REMARK 3 FITTING PROCEDURE : METHOD--A COMBINATION OF MANUAL RIGID-BODY \ REMARK 3 DOCKING AND FLEXIBLE DOCKING REFINEMENT PROTOCOL--A COMBINATION \ REMARK 3 OF MANUAL RIGID-BODY DOCKING AND FLEXIBLE DOCKING \ REMARK 3 \ REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS \ REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL \ REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL \ REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 11.20 \ REMARK 3 NUMBER OF PARTICLES : NULL \ REMARK 3 CTF CORRECTION METHOD : NULL \ REMARK 3 \ REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV \ REMARK 3 \ REMARK 3 OTHER DETAILS: PROJECTION MATCHING USING SPIDER PACKAGE \ REMARK 4 \ REMARK 4 2BCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 \ REMARK 100 \ REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-05. \ REMARK 100 THE DEPOSITION ID IS D_1000034945. \ REMARK 245 \ REMARK 245 EXPERIMENTAL DETAILS \ REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE \ REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) \ REMARK 245 \ REMARK 245 ELECTRON MICROSCOPE SAMPLE \ REMARK 245 SAMPLE TYPE : PARTICLE \ REMARK 245 PARTICLE TYPE : POINT \ REMARK 245 NAME OF SAMPLE : 70S*EF-G*GDP*FUSIDIC ACID \ REMARK 245 COMPLEX; 50S RIBOSOMAL PROTEIN \ REMARK 245 L11; 50S RIBOSOMAL PROTEIN L7/ \ REMARK 245 L12; ELONGATION FACTOR G \ REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 \ REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLEY CARBON FILM \ REMARK 245 GRIDS \ REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE \ REMARK 245 SAMPLE BUFFER : 20MM HEPES-KOH (PH 7.5), 6MM \ REMARK 245 MGCL2, AND 150 MM NH4CL, 2MM \ REMARK 245 SPERMIDINE, 0.4 MM SPERMINE \ REMARK 245 PH : 7.50 \ REMARK 245 SAMPLE DETAILS : ESCHERICHIA COLI 70S RIBOSOME \ REMARK 245 COMPLEXED WITH EF-G (LABELED WITH UNDECAGOLD(UG)),GDP AND \ REMARK 245 FUSIDIC ACID \ REMARK 245 \ REMARK 245 DATA ACQUISITION \ REMARK 245 DATE OF EXPERIMENT : 09-NOV-04 \ REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL \ REMARK 245 TEMPERATURE (KELVIN) : 93.00 \ REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 \ REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM \ REMARK 245 MINIMUM DEFOCUS (NM) : -0.70 \ REMARK 245 MAXIMUM DEFOCUS (NM) : -3.50 \ REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 \ REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 \ REMARK 245 NOMINAL CS : 2.00 \ REMARK 245 IMAGING MODE : BRIGHT FIELD \ REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2000.00 \ REMARK 245 ILLUMINATION MODE : FLOOD BEAM \ REMARK 245 NOMINAL MAGNIFICATION : 50000 \ REMARK 245 CALIBRATED MAGNIFICATION : 50760 \ REMARK 245 SOURCE : FIELD EMISSION GUN \ REMARK 245 ACCELERATION VOLTAGE (KV) : 200 \ REMARK 245 IMAGING DETAILS : NULL \ REMARK 247 \ REMARK 247 ELECTRON MICROSCOPY \ REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON \ REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE \ REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES \ REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION \ REMARK 247 OF THE STRUCTURE FACTORS. \ 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: TRIMERIC \ 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 900 \ REMARK 900 RELATED ENTRIES \ REMARK 900 RELATED ID: 1MMS RELATED DB: PDB \ REMARK 900 N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11 FROM THERMOTOGA MARITIMA \ REMARK 900 RELATED ID: 1CTF RELATED DB: PDB \ REMARK 900 C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI \ REMARK 900 RELATED ID: 1ELO RELATED DB: PDB \ REMARK 900 A PORTION OF G' DOMAIN OF EF-G FROM THERMUS THERMOPHILUS \ DBREF 2BCW A 8 72 UNP P29395 RL11_THEMA 7 71 \ DBREF 2BCW B 53 120 UNP P0A7K2 RL7_ECOLI 53 120 \ DBREF 2BCW C 200 257 UNP P13551 EFG_THETH 200 257 \ SEQRES 1 A 65 GLN ILE LYS LEU GLN LEU PRO ALA GLY LYS ALA THR PRO \ SEQRES 2 A 65 ALA PRO PRO VAL GLY PRO ALA LEU GLY GLN HIS GLY VAL \ SEQRES 3 A 65 ASN ILE MET GLU PHE CYS LYS ARG PHE ASN ALA GLU THR \ SEQRES 4 A 65 ALA ASP LYS ALA GLY MET ILE LEU PRO VAL VAL ILE THR \ SEQRES 5 A 65 VAL TYR GLU ASP LYS SER PHE THR PHE ILE ILE LYS THR \ SEQRES 1 B 68 GLU PHE ASP VAL ILE LEU LYS ALA ALA GLY ALA ASN LYS \ SEQRES 2 B 68 VAL ALA VAL ILE LYS ALA VAL ARG GLY ALA THR GLY LEU \ SEQRES 3 B 68 GLY LEU LYS GLU ALA LYS ASP LEU VAL GLU SER ALA PRO \ SEQRES 4 B 68 ALA ALA LEU LYS GLU GLY VAL SER LYS ASP ASP ALA GLU \ SEQRES 5 B 68 ALA LEU LYS LYS ALA LEU GLU GLU ALA GLY ALA GLU VAL \ SEQRES 6 B 68 GLU VAL LYS \ SEQRES 1 C 58 PRO ILE PRO GLU GLU TYR LEU ASP GLN ALA ARG GLU TYR \ SEQRES 2 C 58 HIS GLU LYS LEU VAL GLU VAL ALA ALA ASP PHE ASP GLU \ SEQRES 3 C 58 ASN ILE MET LEU LYS TYR LEU GLU GLY GLU GLU PRO THR \ SEQRES 4 C 58 GLU GLU GLU LEU VAL ALA ALA ILE ARG LYS GLY THR ILE \ SEQRES 5 C 58 ASP LEU LYS ILE THR PRO \ 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 \ ATOM 1 CA GLN A 8 -36.305 21.282 -86.956 1.00 79.42 C \ ATOM 2 CA ILE A 9 -38.817 20.687 -84.157 1.00 80.39 C \ ATOM 3 CA LYS A 10 -41.901 18.465 -84.029 1.00 77.55 C \ ATOM 4 CA LEU A 11 -44.926 18.346 -81.740 1.00 77.13 C \ ATOM 5 CA GLN A 12 -48.593 17.363 -81.571 1.00 82.10 C \ ATOM 6 CA LEU A 13 -50.789 20.455 -81.253 1.00 79.90 C \ ATOM 7 CA PRO A 14 -54.614 20.325 -81.040 1.00 76.54 C \ ATOM 8 CA ALA A 15 -56.651 21.490 -84.042 1.00 82.83 C \ ATOM 9 CA GLY A 16 -57.753 25.088 -83.500 1.00 98.24 C \ ATOM 10 CA LYS A 17 -55.554 26.155 -80.579 1.00 98.41 C \ ATOM 11 CA ALA A 18 -51.991 27.356 -79.898 1.00 96.77 C \ ATOM 12 CA THR A 19 -49.811 29.920 -78.056 1.00 98.62 C \ ATOM 13 CA PRO A 20 -49.767 28.529 -74.489 1.00100.00 C \ ATOM 14 CA ALA A 21 -46.414 28.649 -72.712 1.00100.00 C \ ATOM 15 CA PRO A 22 -46.433 25.150 -71.173 1.00100.00 C \ ATOM 16 CA PRO A 23 -47.681 23.326 -74.339 1.00100.00 C \ ATOM 17 CA VAL A 24 -46.062 25.310 -77.189 1.00 95.98 C \ ATOM 18 CA GLY A 25 -44.083 28.452 -76.348 1.00 94.07 C \ ATOM 19 CA PRO A 26 -40.961 27.258 -74.435 1.00 93.06 C \ ATOM 20 CA ALA A 27 -40.593 24.229 -76.724 1.00 96.04 C \ ATOM 21 CA LEU A 28 -39.759 25.658 -80.153 1.00 92.03 C \ ATOM 22 CA GLY A 29 -39.737 29.128 -78.637 1.00 88.78 C \ ATOM 23 CA GLN A 30 -36.218 28.237 -77.514 1.00 91.11 C \ ATOM 24 CA HIS A 31 -35.001 27.256 -80.989 1.00 94.53 C \ ATOM 25 CA GLY A 32 -35.661 30.666 -82.524 1.00 90.69 C \ ATOM 26 CA VAL A 33 -39.290 30.336 -83.602 1.00 90.50 C \ ATOM 27 CA ASN A 34 -41.666 33.285 -83.156 1.00 94.89 C \ ATOM 28 CA ILE A 35 -44.683 31.736 -81.400 1.00 97.32 C \ ATOM 29 CA MET A 36 -47.391 34.265 -82.415 1.00 99.82 C \ ATOM 30 CA GLU A 37 -46.762 33.690 -86.139 1.00 92.68 C \ ATOM 31 CA PHE A 38 -47.069 29.905 -85.738 1.00 95.14 C \ ATOM 32 CA CYS A 39 -50.148 29.954 -83.474 1.00 95.64 C \ ATOM 33 CA LYS A 40 -52.226 31.933 -85.973 1.00 96.22 C \ ATOM 34 CA ARG A 41 -50.609 30.131 -88.920 1.00 89.97 C \ ATOM 35 CA PHE A 42 -51.047 26.634 -87.479 1.00 82.17 C \ ATOM 36 CA ASN A 43 -54.590 27.351 -86.310 1.00 86.52 C \ ATOM 37 CA ALA A 44 -55.242 28.663 -89.815 1.00 84.79 C \ ATOM 38 CA GLU A 45 -55.170 25.454 -91.866 1.00 90.10 C \ ATOM 39 CA THR A 46 -55.930 23.326 -88.807 1.00 91.97 C \ ATOM 40 CA ALA A 47 -59.424 24.757 -89.299 1.00 93.30 C \ ATOM 41 CA ASP A 48 -60.326 22.281 -92.044 1.00100.00 C \ ATOM 42 CA LYS A 49 -59.730 19.570 -89.427 1.00 99.10 C \ ATOM 43 CA ALA A 50 -60.759 20.810 -85.974 1.00 93.02 C \ ATOM 44 CA GLY A 51 -61.207 19.004 -82.672 1.00 90.09 C \ ATOM 45 CA MET A 52 -58.497 16.449 -83.398 1.00 88.05 C \ ATOM 46 CA ILE A 53 -54.906 16.434 -82.177 1.00 76.40 C \ ATOM 47 CA LEU A 54 -52.650 16.729 -85.226 1.00 75.31 C \ ATOM 48 CA PRO A 55 -48.819 16.437 -85.291 1.00 73.63 C \ ATOM 49 CA VAL A 56 -46.908 19.171 -87.122 1.00 70.19 C \ ATOM 50 CA VAL A 57 -43.227 19.272 -88.068 1.00 73.93 C \ ATOM 51 CA ILE A 58 -41.886 22.797 -87.667 1.00 77.59 C \ ATOM 52 CA THR A 59 -38.652 23.677 -89.471 1.00 82.77 C \ ATOM 53 CA VAL A 60 -36.638 26.759 -88.485 1.00 85.45 C \ ATOM 54 CA TYR A 61 -34.096 28.279 -90.890 1.00 88.03 C \ ATOM 55 CA GLU A 62 -30.928 30.056 -89.730 1.00 86.30 C \ ATOM 56 CA ASP A 63 -32.839 33.347 -90.043 1.00 83.65 C \ ATOM 57 CA LYS A 64 -35.347 32.274 -87.343 1.00 89.76 C \ ATOM 58 CA SER A 65 -38.039 32.021 -90.036 1.00 87.60 C \ ATOM 59 CA PHE A 66 -39.966 28.765 -90.378 1.00 86.65 C \ ATOM 60 CA THR A 67 -42.382 26.449 -92.192 1.00 79.66 C \ ATOM 61 CA PHE A 68 -44.225 23.357 -91.017 1.00 76.33 C \ ATOM 62 CA ILE A 69 -45.993 20.338 -92.429 1.00 70.90 C \ ATOM 63 CA ILE A 70 -49.259 19.175 -90.883 1.00 65.88 C \ ATOM 64 CA LYS A 71 -49.780 15.407 -90.771 1.00 49.56 C \ ATOM 65 CA THR A 72 -52.639 13.081 -89.898 1.00 48.54 C \ TER 66 THR A 72 \ TER 135 LYS B 120 \ TER 194 PRO C 257 \ MASTER 153 0 0 0 0 0 0 6 191 3 0 16 \ END \ """, "chainA") cmd.hide("all") cmd.color('grey70', "chainA") cmd.show('ribbon', "chainA") cmd.select("e2bcwA1", "c. A & i. 8-70") cmd.center("e2bcwA1", state=0, origin=1) cmd.zoom("e2bcwA1", animate=-1) cmd.show_as('cartoon', "e2bcwA1") cmd.spectrum('count', 'rainbow', "e2bcwA1") cmd.disable("e2bcwA1")