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Database: PDB
Entry: 1LS2
LinkDB: 1LS2
Original site: 1LS2 
HEADER    TRANSLATION/RNA                         16-MAY-02   1LS2              
TITLE     FITTING OF EF-TU AND TRNA IN THE LOW RESOLUTION CRYO-EM MAP           
TITLE    2 OF AN EF-TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND TO            
TITLE    3 E. COLI 70S RIBOSOME                                                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: PHENYLALANINE TRANSFER RNA;                                
COMPND   3 CHAIN: B;                                                            
COMPND   4 MOL_ID: 2;                                                           
COMPND   5 MOLECULE: ELONGATION FACTOR TU;                                      
COMPND   6 CHAIN: A;                                                            
COMPND   7 SYNONYM: EF-TU, P-43                                                 
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;                       
SOURCE   3 ORGANISM_COMMON: BAKER'S YEAST;                                      
SOURCE   4 ORGANISM_TAXID: 4932;                                                
SOURCE   5 MOL_ID: 2;                                                           
SOURCE   6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;                               
SOURCE   7 ORGANISM_TAXID: 562                                                  
KEYWDS    EF-TU, TERNARY COMPLEX, CRYO-EM, 70S E.COLI RIBOSOME,                 
KEYWDS   2 TRANSLATION/RNA COMPLEX                                              
EXPDTA    ELECTRON MICROSCOPY                                                   
MDLTYP    CA ATOMS ONLY, CHAIN A; P ATOMS ONLY, CHAIN B                         
AUTHOR    M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI,N.BURKHARDT,               
AUTHOR   2 K.H.NIERHAUS,R.K.AGRAWAL,J.FRANK                                     
REVDAT   3   24-FEB-09 1LS2    1       VERSN                                    
REVDAT   2   01-APR-03 1LS2    1       JRNL                                     
REVDAT   1   26-JUN-02 1LS2    0                                                
JRNL        AUTH   M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI,                  
JRNL        AUTH 2 N.BURKHARDT,K.H.NIERHAUS,R.K.AGRAWAL,J.FRANK                 
JRNL        TITL   CRYO-EM REVEALS AN ACTIVE ROLE FOR AMINOACYL-TRNA            
JRNL        TITL 2 IN THE ACCOMMODATION PROCESS.                                
JRNL        REF    EMBO J.                       V.  21  3557 2002              
JRNL        REFN                   ISSN 0261-4189                               
JRNL        PMID   12093756                                                     
JRNL        DOI    10.1093/EMBOJ/CDF326                                         
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   H.SONG,M.R.PARSONS,S.ROWSELL,G.LEONARD,S.E.PHILLIPS          
REMARK   1  TITL   CRYSTAL STRUCTURE OF INTACT ELONGATION FACTOR                
REMARK   1  TITL 2 EF-TU FROM E.COLI IN GDP CONFORMATION AT 2.05A               
REMARK   1  TITL 3 RESOLUTION                                                   
REMARK   1  REF    J.MOL.BIOL.                   V. 285  1245 1999              
REMARK   1  REFN                   ISSN 0022-2836                               
REMARK   1 REFERENCE 2                                                          
REMARK   1  AUTH   P.NISSEN,M.KJELDGAARD,S.THIRUP,G.POLEKHINA,                  
REMARK   1  AUTH 2 L.RESHETNIKOVA,B.F.C.CLARK,J.NYBORG                          
REMARK   1  TITL   CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF THE              
REMARK   1  TITL 2 PHE-TRNAPHE, EF-TU, AND A GTP ANALOG                         
REMARK   1  REF    SCIENCE                       V. 270  1464 1995              
REMARK   1  REFN                   ISSN 0036-8075                               
REMARK   1 REFERENCE 3                                                          
REMARK   1  AUTH   H.STARK,M.V.RODNINA,J.RINKE-APPEL,R.BRIMACOMBE,              
REMARK   1  AUTH 2 W.WINTERMEYER,M.VAN HEEL                                     
REMARK   1  TITL   VISUALIZATION OF ELONGATION FACTOR TU ON                     
REMARK   1  TITL 2 ESCHERICHIA COLI RIBOSOME                                    
REMARK   1  REF    NATURE                        V. 389   403 1997              
REMARK   1  REFN                   ISSN 0028-0836                               
REMARK   1 REFERENCE 4                                                          
REMARK   1  AUTH   M.KJELDGAARD,P.NISSEN,S.THIRUP,J.NYBORG                      
REMARK   1  TITL   THE CRYSTAL STRUCTURE OF ELONGATION FACTOR EF-TU             
REMARK   1  TITL 2 FROM THERMUS AQUATICUS IN THE GTP CONFORMATION               
REMARK   1  REF    STRUCTURE                     V.   1    35 1993              
REMARK   1  REFN                   ISSN 0969-2126                               
REMARK   1 REFERENCE 5                                                          
REMARK   1  AUTH   G.POLEKHINA,S.THIRUP,M.KJELDGAARD,P.NISSEN,                  
REMARK   1  AUTH 2 C.LIPPMANN,J.NYBORG                                          
REMARK   1  TITL   HELIX UNWINDING IN THE EFFECTOR REGION OF                    
REMARK   1  TITL 2 ELONGATION FACTOR EF-TU-GDP                                  
REMARK   1  REF    STRUCTURE                     V.   4  1141 1996              
REMARK   1  REFN                   ISSN 0969-2126                               
REMARK   2                                                                      
REMARK   2 RESOLUTION.   16.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   SOFTWARE PACKAGES      : O                                         
REMARK   3   RECONSTRUCTION SCHEMA  : REFERENCE BASED ALIGNMENT                 
REMARK   3                                                                      
REMARK   3 EM MAP-MODEL FITTING AND REFINEMENT                                  
REMARK   3   PDB ENTRY                    : 1EFC/1TTT                           
REMARK   3   REFINEMENT SPACE             : REAL                                
REMARK   3   REFINEMENT PROTOCOL          : NULL                                
REMARK   3   REFINEMENT TARGET            : NULL                                
REMARK   3   OVERALL ANISOTROPIC B VALUE  : NULL                                
REMARK   3                                                                      
REMARK   3 FITTING PROCEDURE : MANUAL                                           
REMARK   3                                                                      
REMARK   3 EM IMAGE RECONSTRUCTION STATISTICS                                   
REMARK   3   NOMINAL PIXEL SIZE (ANGSTROMS)    : NULL                           
REMARK   3   ACTUAL PIXEL SIZE  (ANGSTROMS)    : 2.690                          
REMARK   3   EFFECTIVE RESOLUTION (ANGSTROMS)  : 16.800                         
REMARK   3   NUMBER OF PARTICLES               : 7985                           
REMARK   3   CTF CORRECTION METHOD             : CTF CORRECTION OF 3D-MAPS      
REMARK   3                                                                      
REMARK   3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV                     
REMARK   3                                                                      
REMARK   3 OTHER DETAILS: SPIDER PACKAGE                                        
REMARK   4                                                                      
REMARK   4 1LS2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-02.                  
REMARK 100 THE RCSB ID CODE IS RCSB016233.                                      
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                  : ASYMMETRIC                        
REMARK 245   NAME OF SAMPLE                 : E. COLI 70S RIBOSOME-TERNARY      
REMARK 245                                    COMPLEX-GDP-KIRROMYCIN            
REMARK 245   SAMPLE CONCENTRATION (MG ML-1) : NULL                              
REMARK 245   SAMPLE SUPPORT DETAILS         : NULL                              
REMARK 245   SAMPLE VITRIFICATION DETAILS   : RAPID-FREEZING IN LIQUID          
REMARK 245                                    ETHANE                            
REMARK 245   SAMPLE BUFFER                  : HEPES-KOH BUFFER AT PH 7.5        
REMARK 245   PH                             : 7.50                              
REMARK 245   SAMPLE DETAILS                 : NULL                              
REMARK 245                                                                      
REMARK 245 DATA ACQUISITION                                                     
REMARK 245   DATE OF EXPERIMENT                : 01-MAR-01                      
REMARK 245   NUMBER OF MICROGRAPHS-IMAGES      : NULL                           
REMARK 245   TEMPERATURE (KELVIN)              : 93.00                          
REMARK 245   MICROSCOPE MODEL                  : PHILIPS EM420                  
REMARK 245   DETECTOR TYPE                     : KODAK SO163 FILM               
REMARK 245   MINIMUM DEFOCUS (NM)              : 1000.00                        
REMARK 245   MAXIMUM DEFOCUS (NM)              : 3500.00                        
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)  : 1000.00                        
REMARK 245   ILLUMINATION MODE                 : FLOOD BEAM                     
REMARK 245   NOMINAL MAGNIFICATION             : 50000                          
REMARK 245   CALIBRATED MAGNIFICATION          : 52000                          
REMARK 245   SOURCE                            : LAB6                           
REMARK 245   ACCELERATION VOLTAGE (KV)         : 100                            
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 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1                              
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
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: B, 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     SER A     1                                                      
REMARK 465     LYS A     2                                                      
REMARK 465     GLU A     3                                                      
REMARK 465     LYS A     4                                                      
REMARK 465     PHE A     5                                                      
REMARK 465     GLU A     6                                                      
REMARK 465     ARG A     7                                                      
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1EFC   RELATED DB: PDB                                   
REMARK 900 1EFC IS INTACT ELONGATION FACTOR FROM E.COLI                         
REMARK 900 RELATED ID: 1TTT   RELATED DB: PDB                                   
REMARK 900 1TTT IS PHE-TRNA, ELONGATION FACTOR EF-TU: GDPNP TERNARY             
REMARK 900 COMPLEX                                                              
REMARK 900 RELATED ID: 1EXM   RELATED DB: PDB                                   
REMARK 900 1EXM IS THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS                
REMARK 900 ELONGATION FACTOR TU (EF-TU) IN COMPLEX WITH THE GTP ANALOG          
REMARK 900 GPPNHP.                                                              
REMARK 900 RELATED ID: 1LU3   RELATED DB: PDB                                   
REMARK 900 1LU3 IS THE SEPARATE FITTING OF THE ANTICODON LOOP REGION            
REMARK 900 OF TRNA (NUCLEOTIDE 26-42) IN THE LOW RESOLUTION CRYO-EM             
REMARK 900 MAP OF AN EF-TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND           
REMARK 900 TO E. COLI 70S RIBOSOME                                              
REMARK 900 RELATED ID: EMD-1045   RELATED DB: EMDB                              
DBREF  1LS2 A    1   393  UNP    P0A6N1   EFTU_ECOLI       1    393             
DBREF  1LS2 B    1    76  PDB    1LS2     1LS2             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                  
SEQRES   1 A  393  SER LYS GLU LYS PHE GLU ARG THR LYS PRO HIS VAL ASN          
SEQRES   2 A  393  VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR          
SEQRES   3 A  393  LEU THR ALA ALA ILE THR THR VAL LEU ALA LYS THR TYR          
SEQRES   4 A  393  GLY GLY ALA ALA ARG ALA PHE ASP GLN ILE ASP ASN ALA          
SEQRES   5 A  393  PRO GLU GLU LYS ALA ARG GLY ILE THR ILE ASN THR SER          
SEQRES   6 A  393  HIS VAL GLU TYR ASP THR PRO THR ARG HIS TYR ALA HIS          
SEQRES   7 A  393  VAL ASP CYS PRO GLY HIS ALA ASP TYR VAL LYS ASN MET          
SEQRES   8 A  393  ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU VAL          
SEQRES   9 A  393  VAL ALA ALA THR ASP GLY PRO MET PRO GLN THR ARG GLU          
SEQRES  10 A  393  HIS ILE LEU LEU GLY ARG GLN VAL GLY VAL PRO TYR ILE          
SEQRES  11 A  393  ILE VAL PHE LEU ASN LYS CYS ASP MET VAL ASP ASP GLU          
SEQRES  12 A  393  GLU LEU LEU GLU LEU VAL GLU MET GLU VAL ARG GLU LEU          
SEQRES  13 A  393  LEU SER GLN TYR ASP PHE PRO GLY ASP ASP THR PRO ILE          
SEQRES  14 A  393  VAL ARG GLY SER ALA LEU LYS ALA LEU GLU GLY ASP ALA          
SEQRES  15 A  393  GLU TRP GLU ALA LYS ILE LEU GLU LEU ALA GLY PHE LEU          
SEQRES  16 A  393  ASP SER TYR ILE PRO GLU PRO GLU ARG ALA ILE ASP LYS          
SEQRES  17 A  393  PRO PHE LEU LEU PRO ILE GLU ASP VAL PHE SER ILE SER          
SEQRES  18 A  393  GLY ARG GLY THR VAL VAL THR GLY ARG VAL GLU ARG GLY          
SEQRES  19 A  393  ILE ILE LYS VAL GLY GLU GLU VAL GLU ILE VAL GLY ILE          
SEQRES  20 A  393  LYS GLU THR GLN LYS SER THR CYS THR GLY VAL GLU MET          
SEQRES  21 A  393  PHE ARG LYS LEU LEU ASP GLU GLY ARG ALA GLY GLU ASN          
SEQRES  22 A  393  VAL GLY VAL LEU LEU ARG GLY ILE LYS ARG GLU GLU ILE          
SEQRES  23 A  393  GLU ARG GLY GLN VAL LEU ALA LYS PRO GLY THR ILE LYS          
SEQRES  24 A  393  PRO HIS THR LYS PHE GLU SER GLU VAL TYR ILE LEU SER          
SEQRES  25 A  393  LYS ASP GLU GLY GLY ARG HIS THR PRO PHE PHE LYS GLY          
SEQRES  26 A  393  TYR ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR          
SEQRES  27 A  393  GLY THR ILE GLU LEU PRO GLU GLY VAL GLU MET VAL MET          
SEQRES  28 A  393  PRO GLY ASP ASN ILE LYS MET VAL VAL THR LEU ILE HIS          
SEQRES  29 A  393  PRO ILE ALA MET ASP ASP GLY LEU ARG PHE ALA ILE ARG          
SEQRES  30 A  393  GLU GLY GLY ARG THR VAL GLY ALA GLY VAL VAL ALA LYS          
SEQRES  31 A  393  VAL LEU SER                                                  
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 LINES ARE NOT SHOWN.)
END                                                                             
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