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