HEADER RIBOSOME 26-SEP-02 1MVR TITLE DECODING CENTER & PEPTIDYL TRANSFERASE CENTER FROM THE X-RAY STRUCTURE TITLE 2 OF THE THERMUS THERMOPHILUS 70S RIBOSOME, ALIGNED TO THE LOW TITLE 3 RESOLUTION CRYO-EM MAP OF E.COLI 70S RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRNA, TRIPLET CODON (A-SITE); COMPND 3 CHAIN: 1; COMPND 4 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIX, 30S SUBUNIT; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HELIX 34 OF 16S RRNA; COMPND 7 CHAIN: A; COMPND 8 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIX, 30S SUBUNIT; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HELIX 44 OF 16S RRNA; COMPND 11 CHAIN: B; COMPND 12 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIX, 30S SUBUNIT; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: HELIX 69 OF 23S RRNA; COMPND 15 CHAIN: C; COMPND 16 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIY, 50S SUBUNIT; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: HELIX 89 OF 23S RRNA; COMPND 19 CHAIN: D; COMPND 20 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIY, 50S SUBUNIT; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: HELIX 93 OF 23S RRNA; COMPND 23 CHAIN: E; COMPND 24 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIY, 50S SUBUNIT; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: 30S RIBOSOMAL PROTEIN S12; COMPND 27 CHAIN: O; COMPND 28 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIX, 30S SUBUNIT; COMPND 29 MOL_ID: 8; COMPND 30 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 31 CHAIN: L; COMPND 32 OTHER_DETAILS: BASED ON COORDINATES FROM 1GIY, 50S SUBUNIT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 83333; SOURCE 8 STRAIN: K12; SOURCE 9 MOL_ID: 3; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 ORGANISM_TAXID: 83333; SOURCE 12 STRAIN: K12; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 15 ORGANISM_TAXID: 83333; SOURCE 16 STRAIN: K12; SOURCE 17 MOL_ID: 5; SOURCE 18 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 19 ORGANISM_TAXID: 83333; SOURCE 20 STRAIN: K12; SOURCE 21 MOL_ID: 6; SOURCE 22 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 23 ORGANISM_TAXID: 83333; SOURCE 24 STRAIN: K12; SOURCE 25 MOL_ID: 7; SOURCE 26 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 27 ORGANISM_TAXID: 83333; SOURCE 28 STRAIN: K12; SOURCE 29 MOL_ID: 8; SOURCE 30 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 31 ORGANISM_TAXID: 83333; SOURCE 32 STRAIN: K12 KEYWDS RF2, RELEASE COMPLEX, CONFORMATIONAL CHANGES, RIBOSOME EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN O, L; P ATOMS ONLY, CHAIN 1, A, B, C, D, E AUTHOR U.B.RAWAT,A.V.ZAVIALOV,J.SENGUPTA,M.VALLE,R.A.GRASSUCCI,J.LINDE, AUTHOR 2 B.VESTERGAARD,M.EHRENBERG,J.FRANK REVDAT 5 14-FEB-24 1MVR 1 REMARK REVDAT 4 18-JUL-18 1MVR 1 REMARK REVDAT 3 13-JUL-11 1MVR 1 VERSN REVDAT 2 24-FEB-09 1MVR 1 VERSN REVDAT 1 01-APR-03 1MVR 0 JRNL AUTH U.B.RAWAT,A.V.ZAVIALOV,J.SENGUPTA,M.VALLE,R.A.GRASSUCCI, JRNL AUTH 2 J.LINDE,B.VESTERGAARD,M.EHRENBERG,J.FRANK JRNL TITL A CRYO-ELECTRON MICROSCOPIC STUDY OF RIBOSOME-BOUND JRNL TITL 2 TERMINATION FACTOR RF2 JRNL REF NATURE V. 421 87 2003 JRNL REFN ISSN 0028-0836 JRNL PMID 12511960 JRNL DOI 10.1038/NATURE01224 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.M.YUSUPOV,G.Z.YUSUPOVA,A.BAUCOM,K.LIEBERMAN,T.N.EARNEST, REMARK 1 AUTH 2 J.H.CATE,H.NOLLER REMARK 1 TITL CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION REMARK 1 REF SCIENCE V. 292 883 2001 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.Z.YUSUPOVA,M.M.YUSUPOV,J.H.CATE,H.NOLLER REMARK 1 TITL THE PATH OF MESSENGER RNA THROUGH THE RIBOSOME REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 106 233 2001 REMARK 1 REFN ISSN 0092-8674 REMARK 2 REMARK 2 RESOLUTION. 12.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : O, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1GIX 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 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) : 12.80 REMARK 3 NUMBER OF PARTICLES : 18199 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 1MVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017225. 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 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 32.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL 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 : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 08-NOV-01 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) : 2020.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4500.00 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1, A, B, C, D, E, O, L 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 MET O 1 REMARK 465 VAL O 2 REMARK 465 ALA O 3 REMARK 465 LEU O 4 REMARK 465 ALA O 129 REMARK 465 LYS O 130 REMARK 465 THR O 131 REMARK 465 ALA O 132 REMARK 465 ALA O 133 REMARK 465 LYS O 134 REMARK 465 LYS O 135 REMARK 465 ALA L 2 REMARK 465 LYS L 3 REMARK 465 LYS L 4 REMARK 465 VAL L 5 REMARK 465 ALA L 6 REMARK 465 ALA L 7 REMARK 465 ASP L 141 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GIX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION--30S RIBOSOME REMARK 900 SUBUNIT, THREE TRNA, AND MRNA MOLECULES REMARK 900 RELATED ID: 1GIY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5 A RESOLUTION--50S RIBOSOME REMARK 900 SUBUNIT, THREE TRNA, AND MRNA MOLECULES REMARK 900 RELATED ID: 1MI6 RELATED DB: PDB REMARK 900 DOCKING OF THE MODIFIED RF2 X-RAY STRUCTURE INTO THE LOW RESOLUTION REMARK 900 CRYO-EM MAP OF RF2 E.COLI 70S RIBOSOME COMPLEX REMARK 900 RELATED ID: 1GQE RELATED DB: PDB REMARK 900 POLYPEPTIDE CHAIN RELEASE FACTOR 2 (RF2) FROM E.COLI REMARK 900 RELATED ID: EMD-1006 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-1007 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-1008 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-1009 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-1010 RELATED DB: EMDB DBREF 1MVR O 5 135 UNP Q5SHN3 RS12_THET8 1 131 DBREF 1MVR L 2 141 UNP P29395 RL11_THEMA 1 140 DBREF 1MVR 1 11 13 PDB 1MVR 1MVR 11 13 DBREF 1MVR A 1046 1210 PDB 1MVR 1MVR 1046 1210 DBREF 1MVR B 1400 1500 PDB 1MVR 1MVR 1400 1500 DBREF 1MVR C 1906 1924 PDB 1MVR 1MVR 1906 1924 DBREF 1MVR D 2448 2506 PDB 1MVR 1MVR 2448 2506 DBREF 1MVR E 2583 2609 PDB 1MVR 1MVR 2583 2609 SEQRES 1 1 3 U U U SEQRES 1 A 45 A G G U G C U G C A U G G SEQRES 2 A 45 C C G U C G U C A A C G A SEQRES 3 A 45 C G U C U G G U C A G C A SEQRES 4 A 45 U G G C C C SEQRES 1 B 96 C G C C C G U C A C G C C SEQRES 2 B 96 A U G G G A G C G G G C U SEQRES 3 B 96 C U A C C C G A A G U C G SEQRES 4 B 96 C C G G G A G C C U A C G SEQRES 5 B 96 G G C A G G C G C C G A G SEQRES 6 B 96 G G U A G G G C C C G U G SEQRES 7 B 96 A C U G G G G C G A A G U SEQRES 8 B 96 C G U A A SEQRES 1 C 19 G G C C G U A A C U A U A SEQRES 2 C 19 A C G G U C SEQRES 1 D 59 A U A A C A G G C U G A U SEQRES 2 D 59 C U C C C C C G A G C G U SEQRES 3 D 59 C C A C A G C G G C G G G SEQRES 4 D 59 G A G G U U U G G C A C C SEQRES 5 D 59 U C G A U G U SEQRES 1 E 27 G U U C A G A A C G U C G SEQRES 2 E 27 U G A G A C A G U U C G G SEQRES 3 E 27 U SEQRES 1 O 135 MET VAL ALA LEU PRO THR ILE ASN GLN LEU VAL ARG LYS SEQRES 2 O 135 GLY ARG GLU LYS VAL ARG LYS LYS SER LYS VAL PRO ALA SEQRES 3 O 135 LEU LYS GLY ALA PRO PHE ARG ARG GLY VAL CYS THR VAL SEQRES 4 O 135 VAL ARG THR VAL THR PRO LYS LYS PRO ASN SER ALA LEU SEQRES 5 O 135 ARG LYS VAL ALA LYS VAL ARG LEU THR SER GLY TYR GLU SEQRES 6 O 135 VAL THR ALA TYR ILE PRO GLY GLU GLY HIS ASN LEU GLN SEQRES 7 O 135 GLU HIS SER VAL VAL LEU ILE ARG GLY GLY ARG VAL LYS SEQRES 8 O 135 ASP LEU PRO GLY VAL ARG TYR HIS ILE VAL ARG GLY VAL SEQRES 9 O 135 TYR ASP ALA ALA GLY VAL LYS ASP ARG LYS LYS SER ARG SEQRES 10 O 135 SER LYS TYR GLY THR LYS LYS PRO LYS GLU ALA ALA LYS SEQRES 11 O 135 THR ALA ALA LYS LYS SEQRES 1 L 140 ALA LYS LYS VAL ALA ALA GLN ILE LYS LEU GLN LEU PRO SEQRES 2 L 140 ALA GLY LYS ALA THR PRO ALA PRO PRO VAL GLY PRO ALA SEQRES 3 L 140 LEU GLY GLN HIS GLY VAL ASN ILE MET GLU PHE CYS LYS SEQRES 4 L 140 ARG PHE ASN ALA GLU THR ALA ASP LYS ALA GLY MET ILE SEQRES 5 L 140 LEU PRO VAL VAL ILE THR VAL TYR GLU ASP LYS SER PHE SEQRES 6 L 140 THR PHE ILE ILE LYS THR PRO PRO ALA SER PHE LEU LEU SEQRES 7 L 140 LYS LYS ALA ALA GLY ILE GLU LYS GLY SER SER GLU PRO SEQRES 8 L 140 LYS ARG LYS ILE VAL GLY LYS VAL THR ARG LYS GLN ILE SEQRES 9 L 140 GLU GLU ILE ALA LYS THR LYS MET PRO ASP LEU ASN ALA SEQRES 10 L 140 ASN SER LEU GLU ALA ALA MET LYS ILE ILE GLU GLY THR SEQRES 11 L 140 ALA LYS SER MET GLY ILE GLU VAL VAL ASP CRYST1 P 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