HEADER RIBOSOME 07-AUG-01 1JQT TITLE FITTING OF L11 PROTEIN IN THE LOW RESOLUTION CRYO-EM MAP OF E.COLI 70S TITLE 2 RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: L11 FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL COMPND 5 STRUCTURE OF L11 FROM THERMATOGOMA MARITIMA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS L11, CRYO-EM, 70S E.COLI RIBOSOME, RIBOSOME EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR R.K.AGRAWAL,J.LINDE,J.SEGUPTA,K.H.NIERHAUS,J.FRANK REVDAT 5 07-FEB-24 1JQT 1 REMARK REVDAT 4 24-FEB-09 1JQT 1 VERSN REVDAT 3 01-APR-03 1JQT 1 JRNL REVDAT 2 14-JUN-02 1JQT 1 REMARK REVDAT 1 07-SEP-01 1JQT 0 JRNL AUTH R.K.AGRAWAL,J.LINDE,J.SENGUPTA,K.H.NIERHAUS,J.FRANK JRNL TITL LOCALIZATION OF L11 PROTEIN ON THE RIBOSOME AND ELUCIDATION JRNL TITL 2 OF ITS INVOLVEMENT IN EF-G-DEPENDENT TRANSLOCATION. JRNL REF J.MOL.BIOL. V. 311 777 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11518530 JRNL DOI 10.1006/JMBI.2001.4907 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 DOI 10.1016/S0092-8674(00)80759-X REMARK 1 REFERENCE 2 REMARK 1 AUTH I.S.GABASHVILI,R.K.AGRAWAL,C.M.T.SPAHN,R.A.GRASSUCCI, REMARK 1 AUTH 2 D.I.SVERGUN,J.FRANK,P.PENCZEK REMARK 1 TITL EF-G-DEPENDENT GTP HYDROLYSIS INDUCES SOLUTION STRUCTURE OF REMARK 1 TITL 2 THE E. COLI 70S RIBOSOME AT 11.5A RESOLUTION REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 100 537 2000 REMARK 1 REFN ISSN 0092-8674 REMARK 1 DOI 10.1016/S0092-8674(00)80690-X REMARK 1 REFERENCE 3 REMARK 1 AUTH R.K.AGRAWAL,A.B.HEAGLE,P.PENCZEK,R.A.GRASSUCCI,J.FRANK REMARK 1 TITL EF-G-DEPENDENT GTP HYDROLYSIS INDUCES TRANSLOCATION REMARK 1 TITL 2 ACCOMPANIED BY LARGE CONFORMATIONAL CHANGES IN THE 70S REMARK 1 TITL 3 RIBOSOME REMARK 1 REF NAT.STRUCT.BIOL. V. 6 643 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/10695 REMARK 2 REMARK 2 RESOLUTION. 18.00 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 : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : VISUAL AGREEMENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--MANUAL DETAILS--THIS REMARK 3 STRUCTURE WAS GENERATED BY FITTING THE X-RAY CRYSTAL STRUCTURE REMARK 3 OF L11 INTO THE 70S E. COLI RIBOSOME MAP. L11 (LINKER REGION REMARK 3 BETWEEN N AND C TERMINAL) WAS MODELED TO ACCOMMODATE THE REMARK 3 OBSERVED DENSITIES. CONFORMATIONAL CHANGES OCCUR IN PROTEIN L11 REMARK 3 AND EF-G DUE TO THE BINDING OF EF-G TO THE 70S RIBOSOME. THESE REMARK 3 CHANGED CONFORMATIONS WERE MODELED BASED ON THE FITTING OF THE REMARK 3 CRYSTAL COORDINATES TO THE LOW RESOLUTION RIBOSOME MAP (FACTOR- REMARK 3 BOUND) AND ENERGY MINIMIZING THE FITTED STRUCTURES. 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) : 18.00 REMARK 3 NUMBER OF PARTICLES : 36113 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 1JQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014081. 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) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : NULL REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS EM420 REMARK 245 DETECTOR TYPE : GENERIC FILM REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 52000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : OTHER REMARK 245 ACCELERATION VOLTAGE (KV) : NULL 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: A 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 ALA A -5 REMARK 465 LYS A -4 REMARK 465 LYS A -3 REMARK 465 VAL A -2 REMARK 465 ALA A -1 REMARK 465 ALA A 0 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EG0 RELATED DB: PDB REMARK 900 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5A CRYO-EM REMARK 900 MAP OF THE E.COLI 70S RIBOSOME DBREF 1JQT A -5 133 UNP P29395 RL11_THEMA 1 139 SEQRES 1 A 139 ALA LYS LYS VAL ALA ALA GLN ILE LYS LEU GLN LEU PRO SEQRES 2 A 139 ALA GLY LYS ALA THR PRO ALA PRO PRO VAL GLY PRO ALA SEQRES 3 A 139 LEU GLY GLN HIS GLY VAL ASN ILE MET GLU PHE CYS LYS SEQRES 4 A 139 ARG PHE ASN ALA GLU THR ALA ASP LYS ALA GLY MET ILE SEQRES 5 A 139 LEU PRO VAL VAL ILE THR VAL TYR GLU ASP LYS SER PHE SEQRES 6 A 139 THR PHE ILE ILE LYS THR PRO PRO ALA SER PHE LEU LEU SEQRES 7 A 139 LYS LYS ALA ALA GLY ILE GLU LYS GLY SER SER GLU PRO SEQRES 8 A 139 LYS ARG LYS ILE VAL GLY LYS VAL THR ARG LYS GLN ILE SEQRES 9 A 139 GLU GLU ILE ALA LYS THR LYS MET PRO ASP LEU ASN ALA SEQRES 10 A 139 ASN SER LEU GLU ALA ALA MET LYS ILE ILE GLU GLY THR SEQRES 11 A 139 ALA LYS SER MET GLY ILE GLU VAL VAL 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