HEADER RIBOSOME 20-JUL-13 4BYS OBSLTE 10-DEC-14 4BYS 4V8Y TITLE CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET TITLE 2 EUKARYOTIC TRANSLATION INITIATION COMPLEX SPLIT 4BYL 4BYN 4BYO 4BYP 4BYQ 4BYR 4BYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EUKARYOTIC RIBOSOMAL P_E TRNA; COMPND 3 CHAIN: W SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS RIBOSOME, RIBOSOME INITIATION COMPLEX, INITIATOR FACTOR EIF5B EXPDTA ELECTRON MICROSCOPY AUTHOR I.S.FERNANDEZ,X.C.BAI,T.HUSSAIN,A.C.KELLEY,J.R.LORSCH,V.RAMAKRISHNAN, AUTHOR 2 S.H.W.SCHERES REVDAT 3 10-DEC-14 4BYS 1 OBSLTE REVDAT 2 27-NOV-13 4BYS 1 JRNL REVDAT 1 20-NOV-13 4BYS 0 JRNL AUTH I.S.FERNANDEZ,X.C.BAI,T.HUSSAIN,A.C.KELLEY,J.R.LORSCH, JRNL AUTH 2 V.RAMAKRISHNAN,S.H.SCHERES JRNL TITL MOLECULAR ARCHITECTURE OF A EUKARYOTIC TRANSLATIONAL JRNL TITL 2 INITIATION COMPLEX. JRNL REF SCIENCE V. 342 40585 2013 JRNL REFN ISSN 0036-8075 JRNL PMID 24200810 JRNL DOI 10.1126/SCIENCE.1240585 REMARK 2 REMARK 2 RESOLUTION. 4.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND3, RELION REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : MDFF REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 1.77 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.3 REMARK 3 NUMBER OF PARTICLES : 40729 REMARK 3 CTF CORRECTION METHOD : EACH PARTICLE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: CROSS- REMARK 3 -CORRELATION BETWEEN CRYO-EM MAP AND CRYSTAL STRUCTURE REMARK 3 REMARK 3 OTHER DETAILS: USE A NEWLY DEVELOPED STATISTICAL MOVIE REMARK 3 PROCESSING APPROACH TO COMPENSATE FOR BEAM-INDUCED REMARK 3 MOVEMENT. REMARK 3 SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2421. REMARK 3 (DEPOSITION ID: 11807). REMARK 4 REMARK 4 4BYS 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 13-SEP-13. REMARK 100 THE PDBE ID CODE IS EBI-57753. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : NULL REMARK 245 NAME OF SAMPLE : 80S-EIF5B-MET-ITRNAMET REMARK 245 EUKARYOTIC TRANSLATION REMARK 245 INITIATION COMPLEX REMARK 245 WITH TRNA IN THE PE-SITE REMARK 245 AND ONLY DENSITY FOR THE REMARK 245 G DOMAIN AND DOMAIN II REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.3 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : VITRIFICATION 1 -- REMARK 245 CRYOGEN- ETHANE, HUMIDITY- REMARK 245 100, TEMPERATURE- 90, REMARK 245 INSTRUMENT- FEI VITROBOT REMARK 245 MARK II, METHOD- BLOT 2.5 REMARK 245 SECONDS BEFORE PLUNGING, REMARK 245 SAMPLE BUFFER : 3MM HEPES-KOH, 6.6 MM REMARK 245 TRIS-ACETATE PH 7.2, REMARK 245 3 MM NH4CL, 6.6 MM NH4- REMARK 245 ACETATE, 48 MM K-ACETATE, REMARK 245 4 MM MG-ACETATE, 2. REMARK 245 4 MM DTT REMARK 245 PH : 7.2 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 15-JAN-13 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 1012 REMARK 245 TEMPERATURE (KELVIN) : 85 REMARK 245 MICROSCOPE MODEL : OTHER REMARK 245 DETECTOR TYPE : FEI FALCON (BACKTHINED) REMARK 245 MINIMUM DEFOCUS (NM) : 1900 REMARK 245 MAXIMUM DEFOCUS (NM) : 3900 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) : 16 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 REMARK 245 CALIBRATED MAGNIFICATION : 79096 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 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 QUATERNARY STRUCTURE FOR THIS ENTRY: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: W 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 U W 16 REMARK 465 C W 17 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-2421 RELATED DB: EMDB REMARK 900 MOLECULAR ARCHITECTURE OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 RELATED ID: 4BYL RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYN RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYO RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYP RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYQ RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYR RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYT RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYU RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYV RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYW RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX REMARK 900 RELATED ID: 4BYX RELATED DB: PDB REMARK 900 CRYO-EM RECONSTRUCTION OF THE 80S-EIF5B-MET-ITRNAMET REMARK 900 EUKARYOTIC TRANSLATION INITIATION COMPLEX DBREF 4BYS W 1 76 PDB 4BYS 4BYS 1 76 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 A 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 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