HEADER RIBOSOME 07-AUG-01 1JQM TITLE FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (EF-G) IN THE CRYO-EM TITLE 2 MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G, GDP AND FUSIDIC ACID 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; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ELONGATION FACTOR G; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: EF-G; TRANSLATION ELONGATION FACTOR EF-G; COMPND 10 OTHER_DETAILS: EF-G FROM E. COLI 70S RIBOSOME MODELED BY CRYSTAL COMPND 11 STRUCTURE OF EF-G FROM THERMUS THERMOPHILUS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 6 ORGANISM_TAXID: 562 KEYWDS L11, EF-G, CRYO-EM, 70S E.COLI RIBOSOME, GDP STATE, RIBOSOME EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, B AUTHOR R.K.AGRAWAL,J.LINDE,J.SEGUPTA,K.H.NIERHAUS,J.FRANK REVDAT 5 07-FEB-24 1JQM 1 REMARK SEQADV REVDAT 4 24-FEB-09 1JQM 1 VERSN REVDAT 3 01-APR-03 1JQM 1 JRNL REVDAT 2 14-JUN-02 1JQM 1 REMARK REVDAT 1 07-SEP-01 1JQM 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 J.CZWORKOWSKI,J.WANG,T.A.STEITZ,P.B.MOORE REMARK 1 TITL THE CRYSTAL STRUCTURE OF ELONGATION FACTOR G COMPLEXED WITH REMARK 1 TITL 2 GDP, AT 2.7A RESOLUTION. REMARK 1 REF EMBO J. V. 13 3661 1994 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.AEVARSSON,E.BRAZHNIKOV,M.GARBER,J.ZHELTONOSOVA, REMARK 1 AUTH 2 Y.CHIRGADZE,S.AL-KARADAGHI,L.A.SVENSSON,A.LILJAS REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE RIBOSOMAL TRANSLOCASE: REMARK 1 TITL 2 ELONGATION FACTOR G FROM THERMUS THERMOPHILUS REMARK 1 REF EMBO J. V. 13 3669 1994 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.LAURBERG,O.KRISTENSEN,K.MARTEMYANOV,A.T.GUDKOV,I.NAGAEV, REMARK 1 AUTH 2 D.HUGHES,A.LILJAS REMARK 1 TITL STRUCTURE OF A MUTANT EF-G REVEALS DOMAIN III AND POSSIBLY REMARK 1 TITL 2 THE FUSIDIC ACID BINDING SITE REMARK 1 REF J.MOL.BIOL. V. 303 593 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.2000.4168 REMARK 1 REFERENCE 5 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 AND EF-G INTO THE 70S E. COLI EF-G (GDP FORM) BOUND REMARK 3 RIBOSOME ELECTRON MICROSCOPY MAP. L11 (LINKER REGION BETWEEN N REMARK 3 AND C TERMINAL) AND EF-G POSITIONS OF DOMAINS G AND V WERE REMARK 3 MODELED TO ACCOMMODATE THE CONFORMATIONAL CHANGES. REMARK 3 CONFORMATIONAL CHANGES OCCUR IN PROTEIN L11 AND EF-G IN TWO REMARK 3 STEPS DUE TO THE BINDING OF EF-G TO THE 70S RIBOSOME, AND REMARK 3 SUBSEQUENT GTP HYDROLYSIS. THESE CHANGED CONFORMATIONS WERE REMARK 3 MODELED BASED ON THE FITTING OF THE CRYSTAL COORDINATES TO THE REMARK 3 LOW RESOLUTION RIBOSOME MAP (FACTOR-BOUND) AND ENERGY MINIMIZING REMARK 3 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 1JQM 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_1000014074. 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 : E. COLI 70S RIBOSOME BOUND WITH REMARK 245 EF-G, GDP AND FUSIDIC ACID 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 : 7.60 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 11.5 A CRYO-EM REMARK 900 MAP OF THE E. COLI 70S RIBOSOME DBREF 1JQM A -5 133 UNP P29395 RL11_THEMA 1 139 DBREF 1JQM B 1 691 UNP P13551 EFG_THETH 1 691 SEQADV 1JQM ASN B 208 UNP P13551 GLN 208 CONFLICT 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 SEQRES 1 B 691 MET ALA VAL LYS VAL GLU TYR ASP LEU LYS ARG LEU ARG SEQRES 2 B 691 ASN ILE GLY ILE ALA ALA HIS ILE ASP ALA GLY LYS THR SEQRES 3 B 691 THR THR THR GLU ARG ILE LEU TYR TYR THR GLY ARG ILE SEQRES 4 B 691 HIS LYS ILE GLY GLU VAL HIS GLU GLY ALA ALA THR MET SEQRES 5 B 691 ASP PHE MET GLU GLN GLU ARG GLU ARG GLY ILE THR ILE SEQRES 6 B 691 THR ALA ALA VAL THR THR CYS PHE TRP LYS ASP HIS ARG SEQRES 7 B 691 ILE ASN ILE ILE ASP THR PRO GLY HIS VAL ASP PHE THR SEQRES 8 B 691 ILE GLU VAL GLU ARG SER MET ARG VAL LEU ASP GLY ALA SEQRES 9 B 691 ILE VAL VAL PHE ASP SER SER GLN GLY VAL GLU PRO GLN SEQRES 10 B 691 SER GLU THR VAL TRP ARG GLN ALA GLU LYS TYR LYS VAL SEQRES 11 B 691 PRO ARG ILE ALA PHE ALA ASN LYS MET ASP LYS THR GLY SEQRES 12 B 691 ALA ASP LEU TRP LEU VAL ILE ARG THR MET GLN GLU ARG SEQRES 13 B 691 LEU GLY ALA ARG PRO VAL VAL MET GLN LEU PRO ILE GLY SEQRES 14 B 691 ARG GLU ASP THR PHE SER GLY ILE ILE ASP VAL LEU ARG SEQRES 15 B 691 MET LYS ALA TYR THR TYR GLY ASN ASP LEU GLY THR ASP SEQRES 16 B 691 ILE ARG GLU ILE PRO ILE PRO GLU GLU TYR LEU ASP ASN SEQRES 17 B 691 ALA ARG GLU TYR HIS GLU LYS LEU VAL GLU VAL ALA ALA SEQRES 18 B 691 ASP PHE ASP GLU ASN ILE MET LEU LYS TYR LEU GLU GLY SEQRES 19 B 691 GLU GLU PRO THR GLU GLU GLU LEU VAL ALA ALA ILE ARG SEQRES 20 B 691 LYS GLY THR ILE ASP LEU LYS ILE THR PRO VAL PHE LEU SEQRES 21 B 691 GLY SER ALA LEU LYS ASN LYS GLY VAL GLN LEU LEU LEU SEQRES 22 B 691 ASP ALA VAL VAL ASP TYR LEU PRO SER PRO LEU ASP ILE SEQRES 23 B 691 PRO PRO ILE LYS GLY THR THR PRO GLU GLY GLU VAL VAL SEQRES 24 B 691 GLU ILE HIS PRO ASP PRO ASN GLY PRO LEU ALA ALA LEU SEQRES 25 B 691 ALA PHE LYS ILE MET ALA ASP PRO TYR VAL GLY ARG LEU SEQRES 26 B 691 THR PHE ILE ARG VAL TYR SER GLY THR LEU THR SER GLY SEQRES 27 B 691 SER TYR VAL TYR ASN THR THR LYS GLY ARG LYS GLU ARG SEQRES 28 B 691 VAL ALA ARG LEU LEU ARG MET HIS ALA ASN HIS ARG GLU SEQRES 29 B 691 GLU VAL GLU GLU LEU LYS ALA GLY ASP LEU GLY ALA VAL SEQRES 30 B 691 VAL GLY LEU LYS GLU THR ILE THR GLY ASP THR LEU VAL SEQRES 31 B 691 GLY GLU ASP ALA PRO ARG VAL ILE LEU GLU SER ILE GLU SEQRES 32 B 691 VAL PRO GLU PRO VAL ILE ASP VAL ALA ILE GLU PRO LYS SEQRES 33 B 691 THR LYS ALA ASP GLN GLU LYS LEU SER GLN ALA LEU ALA SEQRES 34 B 691 ARG LEU ALA GLU GLU ASP PRO THR PHE ARG VAL SER THR SEQRES 35 B 691 HIS PRO GLU THR GLY GLN THR ILE ILE SER GLY MET GLY SEQRES 36 B 691 GLU LEU HIS LEU GLU ILE ILE VAL ASP ARG LEU LYS ARG SEQRES 37 B 691 GLU PHE LYS VAL ASP ALA ASN VAL GLY LYS PRO GLN VAL SEQRES 38 B 691 ALA TYR ARG GLU THR ILE THR LYS PRO VAL ASP VAL GLU SEQRES 39 B 691 GLY LYS PHE ILE ARG GLN THR GLY GLY ARG GLY GLN TYR SEQRES 40 B 691 GLY HIS VAL LYS ILE LYS VAL GLU PRO LEU PRO ARG GLY SEQRES 41 B 691 SER GLY PHE GLU PHE VAL ASN ALA ILE VAL GLY GLY VAL SEQRES 42 B 691 ILE PRO LYS GLU TYR ILE PRO ALA VAL GLN LYS GLY ILE SEQRES 43 B 691 GLU GLU ALA MET GLN SER GLY PRO LEU ILE GLY PHE PRO SEQRES 44 B 691 VAL VAL ASP ILE LYS VAL THR LEU TYR ASP GLY SER TYR SEQRES 45 B 691 HIS GLU VAL ASP SER SER GLU MET ALA PHE LYS ILE ALA SEQRES 46 B 691 GLY SER MET ALA ILE LYS GLU ALA VAL GLN LYS GLY ASP SEQRES 47 B 691 PRO VAL ILE LEU GLU PRO ILE MET ARG VAL GLU VAL THR SEQRES 48 B 691 THR PRO GLU GLU TYR MET GLY ASP VAL ILE GLY ASP LEU SEQRES 49 B 691 ASN ALA ARG ARG GLY GLN ILE LEU GLY MET GLU PRO ARG SEQRES 50 B 691 GLY ASN ALA GLN VAL ILE ARG ALA PHE VAL PRO LEU ALA SEQRES 51 B 691 GLU MET PHE GLY TYR ALA THR ASP LEU ARG SER LYS THR SEQRES 52 B 691 GLN GLY ARG GLY SER PHE VAL MET PHE PHE ASP HIS TYR SEQRES 53 B 691 GLN GLU VAL PRO LYS GLN VAL GLN GLU LYS LEU ILE LYS SEQRES 54 B 691 GLY GLN 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