HEADER RIBOSOMAL PROTEIN/RNA 30-SEP-08 3EQ3 TITLE MODEL OF TRNA(TRP)-EF-TU IN THE RIBOSOMAL PRE-ACCOMMODATED STATE TITLE 2 REVEALED BY CRYO-EM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ELONGATION FACTOR TU; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: EF-TU, P-43; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 30S RIBOSOMAL PROTEIN S12; COMPND 7 CHAIN: L; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: 50S RIBOSOMAL PROTEIN L11; COMPND 10 CHAIN: I; COMPND 11 MOL_ID: 4; COMPND 12 MOLECULE: TRNA; COMPND 13 CHAIN: Y; COMPND 14 MOL_ID: 5; COMPND 15 MOLECULE: FRAGMENT H18 OF THE 16S RRNA; COMPND 16 CHAIN: A; COMPND 17 MOL_ID: 6; COMPND 18 MOLECULE: FRAGMENT H44 OF THE 16S RRNA; COMPND 19 CHAIN: C; COMPND 20 MOL_ID: 7; COMPND 21 MOLECULE: FRAGMENT H43-44 OF THE 23S RRNA; COMPND 22 CHAIN: B; COMPND 23 MOL_ID: 8; COMPND 24 MOLECULE: FRAGMENT H95 OF THE 23S RRNA; COMPND 25 CHAIN: D; COMPND 26 MOL_ID: 9; COMPND 27 MOLECULE: FRAGMENT H69 OF THE 23S RRNA; COMPND 28 CHAIN: E SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 6 ORGANISM_TAXID: 83333; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 9 ORGANISM_TAXID: 83333; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 12 ORGANISM_TAXID: 83333; SOURCE 13 MOL_ID: 5; SOURCE 14 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 15 ORGANISM_TAXID: 83333; SOURCE 16 MOL_ID: 6; SOURCE 17 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 18 ORGANISM_TAXID: 83333; SOURCE 19 MOL_ID: 7; SOURCE 20 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 21 ORGANISM_TAXID: 83333; SOURCE 22 MOL_ID: 8; SOURCE 23 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 24 ORGANISM_TAXID: 83333; SOURCE 25 MOL_ID: 9; SOURCE 26 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 27 ORGANISM_TAXID: 83333 KEYWDS PROTEIN TRANSLATION, TERNARY COMPLEX, A/T-TRNA, AUTOMATED DATA KEYWDS 2 COLLECTION, ANTIBIOTIC RESISTANCE, ELONGATION FACTOR, GTP-BINDING, KEYWDS 3 MEMBRANE, METHYLATION, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, PROTEIN KEYWDS 4 BIOSYNTHESIS, RIBONUCLEOPROTEIN, RIBOSOMAL PROTEIN, RNA-BINDING, KEYWDS 5 RRNA-BINDING, TRNA-BINDING, RIBOSOMAL PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN X, L, I; P ATOMS ONLY, CHAIN Y, A, C, B, D, E AUTHOR J.FRANK,W.LI,X.AGIRREZABALA REVDAT 6 21-FEB-24 3EQ3 1 REMARK REVDAT 5 18-JUL-18 3EQ3 1 REMARK REVDAT 4 30-MAY-12 3EQ3 1 REMARK VERSN REVDAT 3 06-JAN-09 3EQ3 1 REMARK REVDAT 2 30-DEC-08 3EQ3 1 JRNL REVDAT 1 16-DEC-08 3EQ3 0 JRNL AUTH W.LI,X.AGIRREZABALA,J.LEI,L.BOUAKAZ,J.L.BRUNELLE, JRNL AUTH 2 R.F.ORTIZ-MEOZ,R.GREEN,S.SANYAL,M.EHRENBERG,J.FRANK JRNL TITL RECOGNITION OF AMINOACYL-TRNA: A COMMON MOLECULAR MECHANISM JRNL TITL 2 REVEALED BY CRYO-EM. JRNL REF EMBO J. V. 27 3322 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 19020518 JRNL DOI 10.1038/EMBOJ.2008.243 REMARK 2 REMARK 2 RESOLUTION. 9.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RSREF, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2AVY REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--SEE METHOD IN THE CITATION REFINEMENT REMARK 3 PROTOCOL--AUTO 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) : 9.000 REMARK 3 NUMBER OF PARTICLES : 290000 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 3EQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049634. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : RIBOSOME IN PRE-ACCOMMODATED REMARK 245 STATE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : A/T-TRNA(TRP), EF-TU, L11, S12, REMARK 245 FRAGMENTS H44 AND H18 FROM THE 16S RRNA, FRAGMENTS H43-H44, H69, REMARK 245 AND H95 FROM THE 23S RRNA REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-JAN-07 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TECNAI F30 REMARK 245 DETECTOR TYPE : GENERIC CCD REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL 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 : 59000 REMARK 245 CALIBRATED MAGNIFICATION : NULL 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 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: NONAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, L, I, Y, A, C, B, D, E 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: 2AVY RELATED DB: PDB REMARK 900 COORDINATES FOR INITIAL INPUT MODEL FOR RSREF REMARK 900 RELATED ID: 2AW4 RELATED DB: PDB REMARK 900 COORDINATES FOR INITIAL INPUT MODEL FOR RSREF REMARK 900 RELATED ID: 1QZA RELATED DB: PDB REMARK 900 COORDINATES FOR INITIAL INPUT MODEL FOR RSREF REMARK 900 RELATED ID: 1OB2 RELATED DB: PDB REMARK 900 COORDINATES FOR INITIAL INPUT MODEL FOR RSREF REMARK 900 RELATED ID: 3EP2 RELATED DB: PDB REMARK 900 MODEL OF PHE-TRNA(PHE) IN THE RIBOSOMAL PRE-ACCOMMODATED STATE REMARK 900 REVEALED BY CRYO-EM REMARK 900 RELATED ID: 3EQ4 RELATED DB: PDB REMARK 900 MODEL OF TRNA(LEU)-EF-TU IN THE RIBOSOMAL PRE-ACCOMMODATED STATE REMARK 900 REVEALED BY CRYO-EM REMARK 900 RELATED ID: EMD-1564 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-1565 RELATED DB: EMDB DBREF 3EQ3 X 1 393 UNP P0A6N1 EFTU_ECOLI 2 394 DBREF 3EQ3 L 1 123 UNP P0A7S3 RS12_ECOLI 2 124 DBREF 3EQ3 I 1 141 UNP P0A7J7 RL11_ECOLI 2 142 DBREF 3EQ3 Y 2 75 PDB 3EQ3 3EQ3 2 75 DBREF 3EQ3 A 526 534 PDB 3EQ3 3EQ3 526 534 DBREF 3EQ3 C 1487 1497 PDB 3EQ3 3EQ3 1487 1497 DBREF 3EQ3 B 1054 1101 PDB 3EQ3 3EQ3 1054 1101 DBREF 3EQ3 D 2647 2674 PDB 3EQ3 3EQ3 2647 2674 DBREF 3EQ3 E 1907 1923 PDB 3EQ3 3EQ3 1907 1923 SEQRES 1 X 393 SER LYS GLU LYS PHE GLU ARG THR LYS PRO HIS VAL ASN SEQRES 2 X 393 VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 X 393 LEU THR ALA ALA ILE THR THR VAL LEU ALA LYS THR TYR SEQRES 4 X 393 GLY GLY ALA ALA ARG ALA PHE ASP GLN ILE ASP ASN ALA SEQRES 5 X 393 PRO GLU GLU LYS ALA ARG GLY ILE THR ILE ASN THR SER SEQRES 6 X 393 HIS VAL GLU TYR ASP THR PRO THR ARG HIS TYR ALA HIS SEQRES 7 X 393 VAL ASP CYS PRO GLY HIS ALA ASP TYR VAL LYS ASN MET SEQRES 8 X 393 ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU VAL SEQRES 9 X 393 VAL ALA ALA THR ASP GLY PRO MET PRO GLN THR ARG GLU SEQRES 10 X 393 HIS ILE LEU LEU GLY ARG GLN VAL GLY VAL PRO TYR ILE SEQRES 11 X 393 ILE VAL PHE LEU ASN LYS CYS ASP MET VAL ASP ASP GLU SEQRES 12 X 393 GLU LEU LEU GLU LEU VAL GLU MET GLU VAL ARG GLU LEU SEQRES 13 X 393 LEU SER GLN TYR ASP PHE PRO GLY ASP ASP THR PRO ILE SEQRES 14 X 393 VAL ARG GLY SER ALA LEU LYS ALA LEU GLU GLY ASP ALA SEQRES 15 X 393 GLU TRP GLU ALA LYS ILE LEU GLU LEU ALA GLY PHE LEU SEQRES 16 X 393 ASP SER TYR ILE PRO GLU PRO GLU ARG ALA ILE ASP LYS SEQRES 17 X 393 PRO PHE LEU LEU PRO ILE GLU ASP VAL PHE SER ILE SER SEQRES 18 X 393 GLY ARG GLY THR VAL VAL THR GLY ARG VAL GLU ARG GLY SEQRES 19 X 393 ILE ILE LYS VAL GLY GLU GLU VAL GLU ILE VAL GLY ILE SEQRES 20 X 393 LYS GLU THR GLN LYS SER THR CYS THR GLY VAL GLU MET SEQRES 21 X 393 PHE ARG LYS LEU LEU ASP GLU GLY ARG ALA GLY GLU ASN SEQRES 22 X 393 VAL GLY VAL LEU LEU ARG GLY ILE LYS ARG GLU GLU ILE SEQRES 23 X 393 GLU ARG GLY GLN VAL LEU ALA LYS PRO GLY THR ILE LYS SEQRES 24 X 393 PRO HIS THR LYS PHE GLU SER GLU VAL TYR ILE LEU SER SEQRES 25 X 393 LYS ASP GLU GLY GLY ARG HIS THR PRO PHE PHE LYS GLY SEQRES 26 X 393 TYR ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR SEQRES 27 X 393 GLY THR ILE GLU LEU PRO GLU GLY VAL GLU MET VAL MET SEQRES 28 X 393 PRO GLY ASP ASN ILE LYS MET VAL VAL THR LEU ILE HIS SEQRES 29 X 393 PRO ILE ALA MET ASP ASP GLY LEU ARG PHE ALA ILE ARG SEQRES 30 X 393 GLU GLY GLY ARG THR VAL GLY ALA GLY VAL VAL ALA LYS SEQRES 31 X 393 VAL LEU SER SEQRES 1 L 123 ALA THR VAL ASN GLN LEU VAL ARG LYS PRO ARG ALA ARG SEQRES 2 L 123 LYS VAL ALA LYS SER ASN VAL PRO ALA LEU GLU ALA CYS SEQRES 3 L 123 PRO GLN LYS ARG GLY VAL CYS THR ARG VAL TYR THR THR SEQRES 4 L 123 THR PRO LYS LYS PRO ASN SER ALA LEU ARG LYS VAL CYS SEQRES 5 L 123 ARG VAL ARG LEU THR ASN GLY PHE GLU VAL THR SER TYR SEQRES 6 L 123 ILE GLY GLY GLU GLY HIS ASN LEU GLN GLU HIS SER VAL SEQRES 7 L 123 ILE LEU ILE ARG GLY GLY ARG VAL LYS ASP LEU PRO GLY SEQRES 8 L 123 VAL ARG TYR HIS THR VAL ARG GLY ALA LEU ASP CYS SER SEQRES 9 L 123 GLY VAL LYS ASP ARG LYS GLN ALA ARG SER LYS TYR GLY SEQRES 10 L 123 VAL LYS ARG PRO LYS ALA SEQRES 1 I 141 ALA LYS LYS VAL GLN ALA TYR VAL LYS LEU GLN VAL ALA SEQRES 2 I 141 ALA GLY MET ALA ASN PRO SER PRO PRO VAL GLY PRO ALA SEQRES 3 I 141 LEU GLY GLN GLN GLY VAL ASN ILE MET GLU PHE CYS LYS SEQRES 4 I 141 ALA PHE ASN ALA LYS THR ASP SER ILE GLU LYS GLY LEU SEQRES 5 I 141 PRO ILE PRO VAL VAL ILE THR VAL TYR ALA ASP ARG SER SEQRES 6 I 141 PHE THR PHE VAL THR LYS THR PRO PRO ALA ALA VAL LEU SEQRES 7 I 141 LEU LYS LYS ALA ALA GLY ILE LYS SER GLY SER GLY LYS SEQRES 8 I 141 PRO ASN LYS ASP LYS VAL GLY LYS ILE SER ARG ALA GLN SEQRES 9 I 141 LEU GLN GLU ILE ALA GLN THR LYS ALA ALA ASP MET THR SEQRES 10 I 141 GLY ALA ASP ILE GLU ALA MET THR ARG SER ILE GLU GLY SEQRES 11 I 141 THR ALA ARG SER MET GLY LEU VAL VAL GLU ASP SEQRES 1 Y 74 C G G A U U U A G C U C A SEQRES 2 Y 74 G U U G G G A G A G C G C SEQRES 3 Y 74 C A G A C U G A A G A U C SEQRES 4 Y 74 U G G A G G U C C U G U G SEQRES 5 Y 74 U U C G A U C C A C A G A SEQRES 6 Y 74 A U U C G C A C C SEQRES 1 A 9 C G C G G U A A U SEQRES 1 C 11 G G G C G A A G U C G SEQRES 1 B 48 A G G A U G U U G G C U U SEQRES 2 B 48 A G A A G C A G C C A U C SEQRES 3 B 48 A U U U A A A G A A A G C SEQRES 4 B 48 G U A A U A G C U SEQRES 1 D 28 U G C U C C U A G U A C G SEQRES 2 D 28 A G A G G A C C G G A G U SEQRES 3 D 28 G G SEQRES 1 E 17 G C C G U A A C U A U A A SEQRES 2 E 17 C G G U 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