HEADER RNA 16-SEP-03 1QZA TITLE COORDINATES OF THE A/T SITE TRNA MODEL FITTED INTO THE CRYO-EM MAP OF TITLE 2 EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHE-TRNA; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS TRNA MODEL, DECODING, A/T-SITE TRNA., RNA EXPDTA ELECTRON MICROSCOPY MDLTYP P ATOMS ONLY, CHAIN B AUTHOR M.VALLE,A.ZAVIALOV,W.LI,S.M.STAGG,J.SENGUPTA,R.C.NIELSEN,P.NISSEN, AUTHOR 2 S.C.HARVEY,M.EHRENBERG,J.FRANK REVDAT 3 14-FEB-24 1QZA 1 REMARK REVDAT 2 24-FEB-09 1QZA 1 VERSN REVDAT 1 04-NOV-03 1QZA 0 JRNL AUTH M.VALLE,A.ZAVIALOV,W.LI,S.M.STAGG,J.SENGUPTA,R.C.NIELSEN, JRNL AUTH 2 P.NISSEN,S.C.HARVEY,M.EHRENBERG,J.FRANK JRNL TITL INCORPORATION OF AMINOACYL-TRNA INTO THE RIBOSOME AS SEEN BY JRNL TITL 2 CRYO-ELECTRON MICROSCOPY JRNL REF NAT.STRUCT.BIOL. V. 10 899 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 14566331 JRNL DOI 10.1038/NSB1003 REMARK 2 REMARK 2 RESOLUTION. 10.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1OB2 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--MANUAL FITTING IN O 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) : 10.00 REMARK 3 NUMBER OF PARTICLES : 75996 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: SPIDER PACKAGE REMARK 4 REMARK 4 1QZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020251. 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 RIBOSOME; TRNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 32.00 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLLEY CARBON FILM REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : POLYMIX BUFFER REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : 70S + FMET-TRNA + PHETRNA + EF REMARK 245 -TU + GDP + KIR MRNA CODES FOR MP-STOP REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL 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) : 2000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : NULL 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 : 49696 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 1OB2 RELATED DB: PDB REMARK 900 E. COLI ELONGATION FACTOR EF-TU COMPLEXED WITH THE ANTIBIOTIC REMARK 900 KIRROMYCIN, A GTP ANALOG, AND PHE-TRNA REMARK 900 RELATED ID: 1QZB RELATED DB: PDB REMARK 900 COORDINATES OF THE A-SITE TRNA MODEL FITTED INTO THE CRYO-EM MAP OF REMARK 900 70S RIBOSOME IN THE PRE-TRANSLOCATIONAL STATE REMARK 900 RELATED ID: 1QZC RELATED DB: PDB REMARK 900 COORDINATES OF S12, SH44, LH69 AND SRL SEPARATELY FITTED INTO THE REMARK 900 CRYO-EM MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN)BOUND 70S REMARK 900 RIBOSOME REMARK 900 RELATED ID: 1QZD RELATED DB: PDB REMARK 900 EF-TU.KIRROMYCIN COORDINATES FITTED INTO THE CRYO-EM MAP OF EF-TU REMARK 900 TERNARY COMPLEX (GDP.KIRROMYCIN)BOUND 70S RIBOSOME REMARK 900 RELATED ID: 1R2W RELATED DB: PDB REMARK 900 COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM REMARK 900 MAP OF THE 70S RIBOSOME REMARK 900 RELATED ID: 1R2X RELATED DB: PDB REMARK 900 COORDINATES OF L11 WITH 58NTS OF 23S RRNA FITTED INTO THE CRYO-EM REMARK 900 MAP OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME REMARK 900 RELATED ID: EMD-1055 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE CONTAINS P ATOMS ONLY DBREF 1QZA B 1 75 PDB 1QZA 1QZA 1 75 SEQRES 1 B 75 G C G G A U U U A G C U C SEQRES 2 B 75 A G U U G G G A G A G C G SEQRES 3 B 75 C C A G A C U G A A G A U SEQRES 4 B 75 C U G G A G G U C C U G U SEQRES 5 B 75 G U U C G A U C C A C A G SEQRES 6 B 75 A A U U C G C A C C 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 P G B 1 -24.604 51.452 -47.785 1.00 37.10 P ATOM 2 P C B 2 -22.560 47.565 -50.981 1.00 0.00 P ATOM 3 P G B 3 -19.739 42.120 -50.271 1.00 0.00 P ATOM 4 P G B 4 -19.552 36.440 -46.055 1.00 0.00 P ATOM 5 P A B 5 -21.173 32.188 -41.018 1.00 0.00 P ATOM 6 P U B 6 -24.381 29.372 -36.707 1.00 0.00 P ATOM 7 P U B 7 -29.927 27.806 -34.668 1.00 0.00 P ATOM 8 P U B 8 -36.011 27.557 -33.938 1.00 0.00 P ATOM 9 P A B 9 -39.932 25.127 -32.665 1.00 0.00 P ATOM 10 P G B 10 -45.490 23.645 -32.338 1.00 0.00 P ATOM 11 P C B 11 -42.126 27.657 -29.337 1.00 0.00 P ATOM 12 P U B 12 -37.610 28.609 -25.970 1.00 0.00 P ATOM 13 P C B 13 -32.136 26.389 -24.891 1.00 0.00 P ATOM 14 P A B 14 -29.218 21.238 -28.901 1.00 0.00 P ATOM 15 P G B 15 -27.223 15.733 -31.578 1.00 0.00 P ATOM 16 P U B 16 -27.016 12.313 -36.378 1.00 0.00 P ATOM 17 P U B 17 -27.326 11.992 -42.221 1.00 0.00 P ATOM 18 P G B 18 -28.394 14.643 -46.927 1.00 0.00 P ATOM 19 P G B 19 -33.871 11.573 -44.790 1.00 0.00 P ATOM 20 P G B 20 -38.064 6.551 -44.178 1.00 0.00 P ATOM 21 P A B 21 -41.717 11.613 -41.541 1.00 0.00 P ATOM 22 P G B 22 -42.126 11.634 -34.331 1.00 0.00 P ATOM 23 P A B 23 -40.583 10.555 -27.786 1.00 0.00 P ATOM 24 P G B 24 -39.377 11.135 -22.148 1.00 0.00 P ATOM 25 P C B 25 -40.644 15.200 -17.716 1.00 0.00 P ATOM 26 P G B 26 -43.855 19.874 -15.996 1.00 0.00 P ATOM 27 P C B 27 -49.311 22.625 -17.327 1.00 0.00 P ATOM 28 P C B 28 -53.882 21.353 -21.036 1.00 0.00 P ATOM 29 P A B 29 -58.838 19.067 -23.494 1.00 0.00 P ATOM 30 P G B 30 -63.013 14.641 -22.119 1.00 0.00 P ATOM 31 P A B 31 -66.043 10.988 -18.336 1.00 0.00 P ATOM 32 P C B 32 -66.924 10.799 -14.263 1.00 0.00 P ATOM 33 P U B 33 -67.867 13.863 -8.776 1.00 0.00 P ATOM 34 P G B 34 -67.177 17.903 -6.064 1.00 0.00 P ATOM 35 P A B 35 -63.937 19.519 -10.485 1.00 0.00 P ATOM 36 P A B 36 -57.948 19.157 -11.951 1.00 0.00 P ATOM 37 P G B 37 -52.379 16.963 -10.622 1.00 0.00 P ATOM 38 P A B 38 -49.474 12.375 -7.984 1.00 0.00 P ATOM 39 P U B 39 -50.202 6.736 -7.874 1.00 0.00 P ATOM 40 P C B 40 -52.368 3.128 -11.870 1.00 0.00 P ATOM 41 P U B 41 -54.242 1.488 -16.381 1.00 0.00 P ATOM 42 P G B 42 -53.534 1.814 -21.904 1.00 0.00 P ATOM 43 P G B 43 -52.210 4.503 -27.390 1.00 0.00 P ATOM 44 P A B 44 -51.312 10.611 -30.869 1.00 0.00 P ATOM 45 P G B 45 -51.605 15.468 -32.986 1.00 0.00 P ATOM 46 P G B 46 -48.719 18.715 -35.203 1.00 0.00 P ATOM 47 P U B 47 -45.894 23.684 -37.084 1.00 0.00 P ATOM 48 P C B 48 -41.348 22.647 -42.021 1.00 0.00 P ATOM 49 P C B 49 -35.673 25.880 -39.819 1.00 0.00 P ATOM 50 P U B 50 -40.688 27.567 -42.595 1.00 0.00 P ATOM 51 P G B 51 -43.258 29.571 -47.495 1.00 0.00 P ATOM 52 P U B 52 -43.475 29.778 -53.229 1.00 0.00 P ATOM 53 P G B 53 -40.169 26.186 -58.189 1.00 0.00 P ATOM 54 P U B 54 -36.416 22.686 -61.345 1.00 0.00 P ATOM 55 P U B 55 -34.002 17.671 -62.012 1.00 0.00 P ATOM 56 P C B 56 -35.642 12.615 -61.499 1.00 0.00 P ATOM 57 P G B 57 -39.689 13.906 -57.695 1.00 0.00 P ATOM 58 P A B 58 -40.338 15.684 -52.607 1.00 0.00 P ATOM 59 P U B 59 -39.405 18.075 -46.936 1.00 0.00 P ATOM 60 P C B 60 -34.663 20.553 -47.045 1.00 0.00 P ATOM 61 P C B 61 -28.255 21.924 -46.596 1.00 0.00 P ATOM 62 P A B 62 -26.057 23.937 -51.197 1.00 0.00 P ATOM 63 P C B 63 -26.114 28.249 -54.910 1.00 0.00 P ATOM 64 P A B 64 -28.534 33.923 -55.347 1.00 0.00 P ATOM 65 P G B 65 -32.342 39.392 -53.123 1.00 0.00 P ATOM 66 P A B 66 -35.304 42.378 -47.724 1.00 0.00 P ATOM 67 P A B 67 -36.429 43.872 -42.221 1.00 0.00 P ATOM 68 P U B 68 -35.061 43.959 -36.052 1.00 0.00 P ATOM 69 P U B 69 -31.431 42.711 -31.457 1.00 0.00 P ATOM 70 P C B 70 -24.485 42.235 -30.365 1.00 0.00 P ATOM 71 P G B 71 -18.649 41.323 -31.441 1.00 0.00 P ATOM 72 P C B 72 -13.515 43.826 -35.551 1.00 0.00 P ATOM 73 P A B 73 -11.378 48.131 -40.556 1.00 0.00 P ATOM 74 P C B 74 -11.518 53.397 -44.780 1.00 0.00 P ATOM 75 P C B 75 -13.042 58.653 -46.853 1.00 0.00 P TER 76 C B 75 MASTER 119 0 0 0 0 0 0 6 75 1 0 6 END