PDB Short entry for 2BCW HEADER RIBOSOME 19-OCT-05 2BCW TITLE COORDINATES OF THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11,C- TITLE 2 TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 AND A PORTION OF THE G' TITLE 3 DOMAIN OF ELONGATION FACTOR G, AS FITTED INTO CRYO-EM MAP OF AN TITLE 4 ESCHERICHIA COLI 70S*EF-G*GDP*FUSIDIC ACID COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 50S RIBOSOMAL PROTEIN L7/L12; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: C-TERMINAL DOMAIN; COMPND 9 SYNONYM: L8; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: ELONGATION FACTOR G; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: A PORTION OF G' DOMAIN'; COMPND 14 SYNONYM: EF-G SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 6 ORGANISM_TAXID: 562; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 9 ORGANISM_TAXID: 274 KEYWDS COMPONENTS INVOLVED IN INTERACTION BETWEEN EF-G AND L7/L12 STALK BASE KEYWDS 2 OF THE RIBOSOME, RIBOSOME EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, B, C AUTHOR P.P.DATTA,M.R.SHARMA,L.QI,J.FRANK,R.K.AGRAWAL REVDAT 4 14-FEB-24 2BCW 1 REMARK REVDAT 3 18-JUL-18 2BCW 1 REMARK REVDAT 2 24-FEB-09 2BCW 1 VERSN REVDAT 1 20-DEC-05 2BCW 0 JRNL AUTH P.P.DATTA,M.R.SHARMA,L.QI,J.FRANK,R.K.AGRAWAL JRNL TITL INTERACTION OF THE G' DOMAIN OF ELONGATION FACTOR G AND THE JRNL TITL 2 C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 DURING JRNL TITL 3 TRANSLOCATION AS REVEALED BY CRYO-EM. JRNL REF MOL.CELL V. 20 723 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 16337596 JRNL DOI 10.1016/J.MOLCEL.2005.10.028 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 PMID 10338213 REMARK 1 DOI 10.1016/S0092-8674(00)80759-X REMARK 1 REFERENCE 2 REMARK 1 AUTH M.LEIJONMARCK,A.LILJAS REMARK 1 TITL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN REMARK 1 TITL 2 L7/L12 FROM ESCHERICHIA COLI AT 1.7 REMARK 1 REF J.MOL.BIOL. V. 195 555 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 3309338 REMARK 1 DOI 10.1016/0022-2836(87)90183-5 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 PMID 8070397 REMARK 2 REMARK 2 RESOLUTION. 11.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : OTHER, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1MMS REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : THE X-RAY CRYSTALLOGRAPHIC REMARK 3 STRUCTURE OF THE EF-G INDIVIDUAL REMARK 3 DOMAINS WERE FITTED INTO THE CRYO- REMARK 3 EM MAP OF THE 70S*EF-G-UG*GDP* REMARK 3 FUSIDIC ACID COMPLEX USING O. THE REMARK 3 G' DOMAIN WITHIN DOMAIN I WAS REMARK 3 SEPARATELY FITTED, USING A REMARK 3 COMBINATION OF MANUAL RIGID-BODY REMARK 3 DOCKING AND FLEXIBLE DOCKING REMARK 3 APPROACHES, AND TAKING INTO REMARK 3 CONSIDERATION BOTH THE CRYO-EM REMARK 3 ENVELOPE AND THE POSITIONAL REMARK 3 CONSTRAINTS IMPOSED BY THE UG REMARK 3 DENSITY. X-RAY CRYSTALLOGRAPHIC REMARK 3 STRUCTURES OF THE N-TERMINAL REMARK 3 DOMAIN OF PROTEIN L11 AND C- REMARK 3 TERMINAL DOMAIN OF PROTEIN L7/L12 REMARK 3 WERE FITTED AS RIGID BODIES. REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--A COMBINATION OF MANUAL RIGID-BODY REMARK 3 DOCKING AND FLEXIBLE DOCKING REFINEMENT PROTOCOL--A COMBINATION REMARK 3 OF MANUAL RIGID-BODY DOCKING AND FLEXIBLE DOCKING 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) : 11.20 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: PROJECTION MATCHING USING SPIDER PACKAGE REMARK 4 REMARK 4 2BCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034945. 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*EF-G*GDP*FUSIDIC ACID REMARK 245 COMPLEX; 50S RIBOSOMAL PROTEIN REMARK 245 L11; 50S RIBOSOMAL PROTEIN L7/ REMARK 245 L12; ELONGATION FACTOR G REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLEY CARBON FILM REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 20MM HEPES-KOH (PH 7.5), 6MM REMARK 245 MGCL2, AND 150 MM NH4CL, 2MM REMARK 245 SPERMIDINE, 0.4 MM SPERMINE REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : ESCHERICHIA COLI 70S RIBOSOME REMARK 245 COMPLEXED WITH EF-G (LABELED WITH UNDECAGOLD(UG)),GDP AND REMARK 245 FUSIDIC ACID REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 09-NOV-04 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) : -0.70 REMARK 245 MAXIMUM DEFOCUS (NM) : -3.50 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 : 50760 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MMS RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11 FROM THERMOTOGA MARITIMA REMARK 900 RELATED ID: 1CTF RELATED DB: PDB REMARK 900 C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 1ELO RELATED DB: PDB REMARK 900 A PORTION OF G' DOMAIN OF EF-G FROM THERMUS THERMOPHILUS DBREF 2BCW A 8 72 UNP P29395 RL11_THEMA 7 71 DBREF 2BCW B 53 120 UNP P0A7K2 RL7_ECOLI 53 120 DBREF 2BCW C 200 257 UNP P13551 EFG_THETH 200 257 SEQRES 1 A 65 GLN ILE LYS LEU GLN LEU PRO ALA GLY LYS ALA THR PRO SEQRES 2 A 65 ALA PRO PRO VAL GLY PRO ALA LEU GLY GLN HIS GLY VAL SEQRES 3 A 65 ASN ILE MET GLU PHE CYS LYS ARG PHE ASN ALA GLU THR SEQRES 4 A 65 ALA ASP LYS ALA GLY MET ILE LEU PRO VAL VAL ILE THR SEQRES 5 A 65 VAL TYR GLU ASP LYS SER PHE THR PHE ILE ILE LYS THR SEQRES 1 B 68 GLU PHE ASP VAL ILE LEU LYS ALA ALA GLY ALA ASN LYS SEQRES 2 B 68 VAL ALA VAL ILE LYS ALA VAL ARG GLY ALA THR GLY LEU SEQRES 3 B 68 GLY LEU LYS GLU ALA LYS ASP LEU VAL GLU SER ALA PRO SEQRES 4 B 68 ALA ALA LEU LYS GLU GLY VAL SER LYS ASP ASP ALA GLU SEQRES 5 B 68 ALA LEU LYS LYS ALA LEU GLU GLU ALA GLY ALA GLU VAL SEQRES 6 B 68 GLU VAL LYS SEQRES 1 C 58 PRO ILE PRO GLU GLU TYR LEU ASP GLN ALA ARG GLU TYR SEQRES 2 C 58 HIS GLU LYS LEU VAL GLU VAL ALA ALA ASP PHE ASP GLU SEQRES 3 C 58 ASN ILE MET LEU LYS TYR LEU GLU GLY GLU GLU PRO THR SEQRES 4 C 58 GLU GLU GLU LEU VAL ALA ALA ILE ARG LYS GLY THR ILE SEQRES 5 C 58 ASP LEU LYS ILE THR PRO 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