HEADER TRANSLATION 13-OCT-15 3JBS TITLE EL6 PROTEIN FROM YEAST 60S RIBOSOMAL SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: EL6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L17, RP18, YL16, 60S RIBOSOMAL PROTEIN L6-A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE BY4741; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 1247190; SOURCE 5 STRAIN: BY4741; SOURCE 6 OTHER_DETAILS: CYTOSOLIC EXTRACT KEYWDS RIBOSOME, TRANSLATION EXPDTA ELECTRON MICROSCOPY AUTHOR D.O.PASSOS,D.LYUMKIS REVDAT 4 21-FEB-24 3JBS 1 REMARK REVDAT 3 18-JUL-18 3JBS 1 REMARK REVDAT 2 18-NOV-15 3JBS 1 JRNL REVDAT 1 28-OCT-15 3JBS 0 JRNL AUTH D.O.PASSOS,D.LYUMKIS JRNL TITL SINGLE-PARTICLE CRYOEM ANALYSIS AT NEAR-ATOMIC RESOLUTION JRNL TITL 2 FROM SEVERAL THOUSAND ASYMMETRIC SUBUNITS. JRNL REF J.STRUCT.BIOL. V. 192 235 2015 JRNL REFN ISSN 1047-8477 JRNL PMID 26470814 JRNL DOI 10.1016/J.JSB.2015.10.002 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : ROSETTA, UCSF CHIMERA, FREALIGN REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 4UJQ REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : FSC REMARK 3 OVERALL ANISOTROPIC B VALUE : 50.000 REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--FLEXIBLE REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.310 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.900 REMARK 3 NUMBER OF PARTICLES : 75653 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: B-FACTOR OF -50 APPLIED TO FINAL MAP (SINGLE REMARK 3 PARTICLE--APPLIED SYMMETRY: C1). REMARK 4 REMARK 4 3JBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000160502. 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 : SACCHAROMYCES CEREVISIAE LARGE REMARK 245 60S RIBOSOMAL SUBUNIT REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : 400 MESH, 1.2X1.3 MICRON C-FLAT REMARK 245 GRIDS, PLASMA-TREATED FOR 5 REMARK 245 SECONDS REMARK 245 SAMPLE VITRIFICATION DETAILS : A 3 UL SAMPLE WAS APPLIED ONTO REMARK 245 A FRESHLY PLASMA-TREATED (6 REMARK 245 SECONDS, GATAN SOLARUS PLASMA REMARK 245 CLEANER) HOLEY CARBON C-FLAT REMARK 245 GRID (PROTOCHIPS, INC.), REMARK 245 ALLOWING THE SAMPLE TO ADSORB REMARK 245 FOR 30 SECONDS. THE SAMPLE WAS REMARK 245 THEN PLUNGE-FROZEN IN LIQUID REMARK 245 ETHANE USING A MANUAL CRYO- REMARK 245 PLUNGER IN AMBIENT ATMOSPHERE REMARK 245 AT 4 DEGREES C. REMARK 245 SAMPLE BUFFER : ELUTION BUFFER (50 MM HEPES REMARK 245 -KOH, 100 MM KOAC, 5 MM MGOAC, REMARK 245 1 MM EDTA, 2 MM DTT) REMARK 245 PH : 6.80 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 02-SEP-14 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K2 (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 22500 REMARK 245 CALIBRATED MAGNIFICATION : 38167 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : SUPER-RESOLUTION IMAGING 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 171 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 36 124.01 -39.39 REMARK 500 ASN A 72 16.18 -141.96 REMARK 500 LYS A 110 74.73 -66.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-6478 RELATED DB: EMDB DBREF 3JBS A 1 176 UNP Q02326 RL6A_YEAST 1 176 SEQRES 1 A 176 MET SER ALA GLN LYS ALA PRO LYS TRP TYR PRO SER GLU SEQRES 2 A 176 ASP VAL ALA ALA LEU LYS LYS THR ARG LYS ALA ALA ARG SEQRES 3 A 176 PRO GLN LYS LEU ARG ALA SER LEU VAL PRO GLY THR VAL SEQRES 4 A 176 LEU ILE LEU LEU ALA GLY ARG PHE ARG GLY LYS ARG VAL SEQRES 5 A 176 VAL TYR LEU LYS HIS LEU GLU ASP ASN THR LEU LEU ILE SEQRES 6 A 176 SER GLY PRO PHE LYS VAL ASN GLY VAL PRO LEU ARG ARG SEQRES 7 A 176 VAL ASN ALA ARG TYR VAL ILE ALA THR SER THR LYS VAL SEQRES 8 A 176 SER VAL GLU GLY VAL ASN VAL GLU LYS PHE ASN VAL GLU SEQRES 9 A 176 TYR PHE ALA LYS GLU LYS LEU THR LYS LYS GLU LYS LYS SEQRES 10 A 176 GLU ALA ASN LEU PHE PRO GLU GLN GLN ASN LYS GLU ILE SEQRES 11 A 176 LYS ALA GLU ARG VAL GLU ASP GLN LYS VAL VAL ASP LYS SEQRES 12 A 176 ALA LEU ILE ALA GLU ILE LYS LYS THR PRO LEU LEU LYS SEQRES 13 A 176 GLN TYR LEU SER ALA SER PHE SER LEU LYS ASN GLY ASP SEQRES 14 A 176 LYS PRO HIS MET LEU LYS PHE HELIX 1 1 PRO A 68 GLY A 73 1 6 HELIX 2 2 ASN A 80 ARG A 82 5 3 HELIX 3 3 THR A 112 PHE A 122 1 11 HELIX 4 4 PRO A 123 GLN A 126 5 4 HELIX 5 5 LYS A 131 LYS A 150 1 20 HELIX 6 6 LEU A 154 ALA A 161 1 8 SHEET 1 A 5 ARG A 77 VAL A 79 0 SHEET 2 A 5 LEU A 63 SER A 66 -1 N LEU A 63 O VAL A 79 SHEET 3 A 5 ARG A 51 HIS A 57 -1 N VAL A 53 O SER A 66 SHEET 4 A 5 THR A 38 LEU A 42 -1 N LEU A 40 O VAL A 52 SHEET 5 A 5 VAL A 84 LYS A 90 -1 O THR A 89 N VAL A 39 CISPEP 1 GLY A 67 PRO A 68 0 -0.48 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