HEADER RIBOSOME 05-APR-14 4CXB OBSLTE 10-DEC-14 4CXB 4UJE TITLE REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY 40S SUBUNIT TITLE 2 ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REARRANGEMENT SPLIT 4CXB 4CXC 4CXD 4CXE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-LYS; COMPND 3 CHAIN: V; COMPND 4 OTHER_DETAILS: FOR MODELING E.COLI TRNAPHE (CHAIN C, PDB ID CODE COMPND 5 3I8G) WAS USED.; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TRNA-PHE; COMPND 8 CHAIN: W; COMPND 9 OTHER_DETAILS: FOR MODELING E.COLI TRNAPHE (CHAIN D, PDB ID CODE COMPND 10 3I8G) WAS USED.; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: MESSENGER RNA; COMPND 13 CHAIN: X; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: FOR MODELING MRNA (CHAIN 1, PDB ID CODE 3I8G) WAS COMPND 16 USED. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 7 ORGANISM_COMMON: CATTLE; SOURCE 8 ORGANISM_TAXID: 9913; SOURCE 9 ORGAN: LIVER; SOURCE 10 MOL_ID: 3; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBOSOME, TRANSLATION, MAMMALIAN 80S RIBOSOME, ELONGATION CYCLE, KEYWDS 2 POST-TRANSLOCATIONAL STATE, TRNA SELECTION EXPDTA ELECTRON MICROSCOPY AUTHOR T.V.BUDKEVICH,J.GIESEBRECHT,E.BEHRMANN,J.LOERKE,D.J.F.RAMRATH, AUTHOR 2 T.MIELKE,J.ISMER,P.HILDEBRAND,C.-S.TUNG,K.H.NIERHAUS, AUTHOR 3 K.Y.SANBONMATSU,C.M.T.SPAHN REVDAT 2 10-DEC-14 4CXB 1 OBSLTE REVDAT 1 16-JUL-14 4CXB 0 JRNL AUTH T.V.BUDKEVICH,J.GIESEBRECHT,E.BEHRMANN,J.LOERKE,D.J.RAMRATH, JRNL AUTH 2 T.MIELKE,J.ISMER,P.W.HILDEBRAND,C.S.TUNG,K.H.NIERHAUS, JRNL AUTH 3 K.Y.SANBONMATSU,C.M.SPAHN JRNL TITL REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY SUBUNIT JRNL TITL 2 ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REARRANGEMENT. JRNL REF CELL(CAMBRIDGE,MASS.) V. 158 121 2014 JRNL REFN ISSN 0092-8674 JRNL PMID 24995983 JRNL DOI 10.1016/J.CELL.2014.04.044 REMARK 2 REMARK 2 RESOLUTION. 6.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : SPIDER, SPARX REMARK 3 RECONSTRUCTION SCHEMA : MULTI-REFERENCE TEMPLATE MATCHING REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : CORRELATION REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : MDFIT REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.26 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 1.26 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 6.9 REMARK 3 NUMBER OF PARTICLES : 236113 REMARK 3 CTF CORRECTION METHOD : DEFOCUS GROUP REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: CROSS- REMARK 3 -CORRELATION WITH KNOWN STRUCTURE REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 3 SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2620. REMARK 3 (DEPOSITION ID: 12402). REMARK 4 REMARK 4 4CXB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 THIS ENTRY WITH OTHER SPLIT ENTRIES HAVE BEEN CONSOLIDATED INTO A REMARK 5 COMBINED FILE FOR COMPLETE REPRESENTATION. NO COORDINATES HAVE BEEN REMARK 5 CHANGED. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-APR-14. REMARK 100 THE PDBE ID CODE IS EBI-60174. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : CRYO-EM REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : NULL REMARK 245 NAME OF SAMPLE : POST-TRANSLOCATIONAL RABBIT REMARK 245 80S RIBOSOME WITH REMARK 245 TWO TRNAS AND MRNA BOUND REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.38 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- REMARK 245 CRYOGEN- ETHANE, HUMIDITY- 80, REMARK 245 INSTRUMENT- FEI VITROBOT MARK REMARK 245 II, METHOD- BLOT FOR 2 SECONDS REMARK 245 BEFORE PLUNGING REMARK 245 SAMPLE BUFFER : 20MM HEPES-KOH, 5MM MGCL2, 100 MM REMARK 245 NH4CL, 6 MM BETA-MERCAPTOETHANOL, REMARK 245 0.8 MM SPERMIDINE, 0.6 MM REMARK 245 SPERMINE REMARK 245 PH : 7.5 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 02-JUN-08 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 826 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 2000 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 39000 REMARK 245 CALIBRATED MAGNIFICATION : 65520 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : MINIMAL DOSE SYSTEM 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 QUATERNARY STRUCTURE FOR THIS ENTRY: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: V, W, X 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: EMD-2620 RELATED DB: EMDB REMARK 900 RELATED ID: 4CXC RELATED DB: PDB REMARK 900 REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY 40S REMARK 900 SUBUNIT ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REMARK 900 REARRANGEMENT REMARK 900 RELATED ID: 4CXD RELATED DB: PDB REMARK 900 REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY 40S REMARK 900 SUBUNIT ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REMARK 900 REARRANGEMENT REMARK 900 RELATED ID: 4CXE RELATED DB: PDB REMARK 900 REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY 40S REMARK 900 SUBUNIT ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REMARK 900 REARRANGEMENT REMARK 900 RELATED ID: 4CXG RELATED DB: PDB REMARK 900 REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY 40S REMARK 900 SUBUNIT ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REMARK 900 REARRANGEMENT REMARK 900 RELATED ID: 4CXH RELATED DB: PDB REMARK 900 REGULATION OF THE MAMMALIAN ELONGATION CYCLE BY 40S REMARK 900 SUBUNIT ROLLING: A EUKARYOTIC-SPECIFIC RIBOSOME REMARK 900 REARRANGEMENT DBREF 4CXB V 1 76 PDB 4CXB 4CXB 1 76 DBREF 4CXB W 1 76 PDB 4CXB 4CXB 1 76 DBREF 4CXB X 34 61 PDB 4CXB 4CXB 34 61 SEQRES 1 V 76 G C C C G G A U A G C U C SEQRES 2 V 76 A G U C G G U A G A G C A SEQRES 3 V 76 G G G G A U U G A A A A U SEQRES 4 V 76 C C C C G U G U C C U U G SEQRES 5 V 76 G U U C G A U U C C G A G SEQRES 6 V 76 U C C G G G C A C C A SEQRES 1 W 76 G C C C G G A U A G C U C SEQRES 2 W 76 A G U C G G U A G A G C A SEQRES 3 W 76 G G G G A U U G A A MIA A U SEQRES 4 W 76 C C C C G U G U C C U U G SEQRES 5 W 76 G U U C G A U U C C G A G SEQRES 6 W 76 U C C G G G C A C C A SEQRES 1 X 28 U U U U U U U U U U U U U SEQRES 2 X 28 U U U U U U U U U U U U U SEQRES 3 X 28 U U MODRES 4CXB MIA W 37 A HET MIA W 37 29 HETNAM MIA 2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE FORMUL 2 MIA C16 H26 N5 O7 P S LINK O3' A W 36 P MIA W 37 1555 1555 1.52 LINK O3' MIA W 37 P A W 38 1555 1555 1.64 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