HEADER RNA 16-SEP-03 1QZB TITLE COORDINATES OF THE A-SITE TRNA MODEL FITTED INTO THE CRYO-EM MAP OF TITLE 2 70S RIBOSOME IN THE PRE-TRANSLOCATIONAL STATE 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 A-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 1QZB 1 REMARK REVDAT 2 24-FEB-09 1QZB 1 VERSN REVDAT 1 04-NOV-03 1QZB 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. 9.00 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) : 9.000 REMARK 3 NUMBER OF PARTICLES : 52181 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 1QZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020252. 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 BEARING DEACYLATED TRNAFMET REMARK 245 IN THE P SITE AND DIPEPTIDYL MP-TRNA IN THE A SITE. SAME COMPLEX REMARK 245 AS IN PROJECT 138 BUT IN THE ABSENCE OF KIRROMICIN. THE PHE-TRNA REMARK 245 IS FULLY DELIVERED TO THE A-SITE AND AFTER THE PEPTIDE BOND REMARK 245 FORMATION THE DIPEPTIDYL-TRNA STAYS IN THE A SITE. MRNA CODES REMARK 245 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 : 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 : 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 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 G B 1 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: 1QZA RELATED DB: PDB REMARK 900 COORDINATES OF THE A/T SITE TRNA MODEL FITTED INTO THE CRYO-EM MAP REMARK 900 OF EF-TU TERNARY COMPLEX (GDP.KIRROMYCIN) BOUND 70S RIBOSOME 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-1056 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE CONTAINS P ATOMS ONLY DBREF 1QZB B 1 76 PDB 1QZB 1QZB 1 76 SEQRES 1 B 76 G C G G A U U U A G C U C SEQRES 2 B 76 A G U U G G G A G A G C G SEQRES 3 B 76 C C A G A C U G A A G A U SEQRES 4 B 76 C U G G A G G U C C U G U SEQRES 5 B 76 G U U C G A U C C A C A G SEQRES 6 B 76 A A U U C G C A C C A 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 C B 2 -5.758 0.226 -37.611 1.00 36.15 P ATOM 2 P G B 3 -7.548 -4.817 -35.780 1.00 38.57 P ATOM 3 P G B 4 -11.932 -7.551 -32.336 1.00 50.13 P ATOM 4 P A B 5 -16.795 -7.912 -28.958 1.00 46.12 P ATOM 5 P U B 6 -21.805 -6.611 -26.755 1.00 41.93 P ATOM 6 P U B 7 -26.975 -3.593 -26.744 1.00 39.61 P ATOM 7 P U B 8 -31.089 2.030 -27.580 1.00 38.44 P ATOM 8 P A B 9 -35.423 2.775 -28.335 1.00 30.30 P ATOM 9 P G B 10 -39.050 8.345 -28.654 1.00 36.63 P ATOM 10 P C B 11 -34.755 8.904 -24.262 1.00 48.28 P ATOM 11 P U B 12 -32.369 6.465 -19.720 1.00 38.23 P ATOM 12 P C B 13 -31.272 1.173 -17.685 1.00 37.44 P ATOM 13 P A B 14 -31.981 -5.471 -20.177 1.00 33.32 P ATOM 14 P G B 15 -33.645 -10.686 -23.328 1.00 33.55 P ATOM 15 P U B 16 -34.340 -13.695 -27.700 1.00 58.67 P ATOM 16 P U B 17 -33.883 -16.686 -32.752 1.00 63.01 P ATOM 17 P G B 18 -31.259 -15.909 -38.418 1.00 51.43 P ATOM 18 P G B 19 -37.225 -13.180 -38.500 1.00 56.66 P ATOM 19 P G B 20 -43.864 -11.829 -38.957 1.00 82.09 P ATOM 20 P A B 21 -43.635 -6.120 -36.923 1.00 46.40 P ATOM 21 P G B 22 -46.276 -4.974 -30.765 1.00 19.04 P ATOM 22 P A B 23 -47.138 -2.794 -24.117 1.00 28.32 P ATOM 23 P G B 24 -48.093 -1.758 -18.840 1.00 33.68 P ATOM 24 P C B 25 -47.497 2.456 -15.297 1.00 50.66 P ATOM 25 P G B 26 -46.529 8.123 -14.354 1.00 60.43 P ATOM 26 P C B 27 -46.631 13.381 -17.559 1.00 88.39 P ATOM 27 P C B 28 -50.041 15.583 -21.816 1.00108.26 P ATOM 28 P A B 29 -55.442 16.471 -23.178 1.00132.50 P ATOM 29 P G B 30 -61.462 15.138 -21.832 1.00164.78 P ATOM 30 P A B 31 -66.694 12.686 -19.173 1.00172.07 P ATOM 31 P C B 32 -67.465 12.084 -14.147 1.00176.80 P ATOM 32 P U B 33 -68.159 13.437 -8.953 1.00200.00 P ATOM 33 P G B 34 -67.519 18.178 -6.035 1.00193.77 P ATOM 34 P A B 35 -64.029 19.550 -9.947 1.00185.75 P ATOM 35 P A B 36 -57.782 18.089 -10.796 1.00196.33 P ATOM 36 P G B 37 -52.701 16.655 -10.766 1.00200.00 P ATOM 37 P A B 38 -50.476 11.124 -9.444 1.00193.90 P ATOM 38 P U B 39 -50.948 5.622 -8.416 1.00171.33 P ATOM 39 P C B 40 -54.795 1.745 -11.425 1.00160.10 P ATOM 40 P U B 41 -58.057 -0.588 -15.208 1.00138.03 P ATOM 41 P G B 42 -59.186 -0.594 -20.774 1.00119.52 P ATOM 42 P G B 43 -57.754 1.195 -26.794 1.00 93.55 P ATOM 43 P A B 44 -53.639 3.584 -31.333 1.00 91.74 P ATOM 44 P G B 45 -49.295 5.893 -33.760 1.00 78.71 P ATOM 45 P G B 46 -43.788 6.888 -33.961 1.00 60.98 P ATOM 46 P U B 47 -37.838 6.244 -35.147 1.00 78.20 P ATOM 47 P C B 48 -35.552 0.173 -37.919 1.00 52.65 P ATOM 48 P C B 49 -30.710 -0.642 -33.151 1.00 17.11 P ATOM 49 P U B 50 -31.003 2.711 -37.547 1.00 17.58 P ATOM 50 P G B 51 -30.216 3.602 -43.159 1.00 21.85 P ATOM 51 P U B 52 -28.755 2.168 -48.651 1.00 7.73 P ATOM 52 P G B 53 -27.240 -2.779 -52.407 1.00 11.78 P ATOM 53 P U B 54 -26.502 -8.282 -54.350 1.00 17.41 P ATOM 54 P U B 55 -28.779 -13.145 -54.296 1.00 30.57 P ATOM 55 P C B 56 -33.926 -14.897 -54.061 1.00 40.60 P ATOM 56 P G B 57 -35.724 -10.053 -52.490 1.00 37.48 P ATOM 57 P A B 58 -35.429 -6.974 -47.533 1.00 32.55 P ATOM 58 P U B 59 -34.995 -4.688 -41.776 1.00 48.23 P ATOM 59 P C B 60 -30.358 -6.402 -39.602 1.00 26.95 P ATOM 60 P C B 61 -25.991 -10.032 -36.513 1.00 28.80 P ATOM 61 P A B 62 -21.743 -11.751 -39.587 1.00 25.23 P ATOM 62 P C B 63 -17.611 -9.879 -42.987 1.00 28.44 P ATOM 63 P A B 64 -14.912 -4.910 -45.463 1.00 30.74 P ATOM 64 P G B 65 -14.792 1.623 -43.525 1.00 13.07 P ATOM 65 P A B 66 -16.376 5.987 -38.708 1.00 22.92 P ATOM 66 P A B 67 -18.028 9.316 -34.410 1.00 22.81 P ATOM 67 P U B 68 -18.743 10.679 -28.875 1.00 45.82 P ATOM 68 P U B 69 -17.308 8.873 -23.402 1.00 51.04 P ATOM 69 P C B 70 -13.801 4.791 -20.033 1.00 50.83 P ATOM 70 P G B 71 -9.372 1.245 -18.842 1.00 54.67 P ATOM 71 P C B 72 -3.810 -1.314 -20.206 1.00 59.46 P ATOM 72 P A B 73 0.567 -1.911 -22.800 1.00 59.61 P ATOM 73 P C B 74 4.732 -2.057 -20.714 1.00 59.61 P ATOM 74 P C B 75 9.331 -7.269 -18.282 1.00 55.58 P ATOM 75 P A B 76 14.175 -6.671 -16.870 1.00 59.61 P TER 76 A B 76 MASTER 131 0 0 0 0 0 0 6 75 1 0 6 END