1LS2 - Header Asymmetric Unit

HEADER TRANSLATION/RNA 16-MAY-02 1LS2

TITLE FITTING OF EF-TU AND TRNA IN THE LOW RESOLUTION CRYO-EM MAP TITLE 2 OF AN EF-TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND TO TITLE 3 E. COLI 70S RIBOSOME

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHENYLALANINE TRANSFER RNA; COMPND 3 CHAIN: B; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: ELONGATION FACTOR TU; COMPND 6 CHAIN: A; COMPND 7 SYNONYM: EF-TU, P-43

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562

KEYWDS EF-TU, TERNARY COMPLEX, CRYO-EM, 70S E.COLI RIBOSOME, KEYWDS 2 TRANSLATION/RNA COMPLEX

EXPDTA ELECTRON MICROSCOPY

MDLTYP CA ATOMS ONLY, CHAIN A; P ATOMS ONLY, CHAIN B

AUTHOR M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI,N.BURKHARDT, AUTHOR 2 K.H.NIERHAUS,R.K.AGRAWAL,J.FRANK

REVDAT 3 24-FEB-09 1LS2 1 VERSN REVDAT 2 01-APR-03 1LS2 1 JRNL REVDAT 1 26-JUN-02 1LS2 0

JRNL AUTH M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI, JRNL AUTH 2 N.BURKHARDT,K.H.NIERHAUS,R.K.AGRAWAL,J.FRANK JRNL TITL CRYO-EM REVEALS AN ACTIVE ROLE FOR AMINOACYL-TRNA JRNL TITL 2 IN THE ACCOMMODATION PROCESS. JRNL REF EMBO J. V. 21 3557 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12093756 JRNL DOI 10.1093/EMBOJ/CDF326

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.SONG,M.R.PARSONS,S.ROWSELL,G.LEONARD,S.E.PHILLIPS REMARK 1 TITL CRYSTAL STRUCTURE OF INTACT ELONGATION FACTOR REMARK 1 TITL 2 EF-TU FROM E.COLI IN GDP CONFORMATION AT 2.05A REMARK 1 TITL 3 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 285 1245 1999 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.NISSEN,M.KJELDGAARD,S.THIRUP,G.POLEKHINA, REMARK 1 AUTH 2 L.RESHETNIKOVA,B.F.C.CLARK,J.NYBORG REMARK 1 TITL CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF THE REMARK 1 TITL 2 PHE-TRNAPHE, EF-TU, AND A GTP ANALOG REMARK 1 REF SCIENCE V. 270 1464 1995 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.STARK,M.V.RODNINA,J.RINKE-APPEL,R.BRIMACOMBE, REMARK 1 AUTH 2 W.WINTERMEYER,M.VAN HEEL REMARK 1 TITL VISUALIZATION OF ELONGATION FACTOR TU ON REMARK 1 TITL 2 ESCHERICHIA COLI RIBOSOME REMARK 1 REF NATURE V. 389 403 1997 REMARK 1 REFN ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.KJELDGAARD,P.NISSEN,S.THIRUP,J.NYBORG REMARK 1 TITL THE CRYSTAL STRUCTURE OF ELONGATION FACTOR EF-TU REMARK 1 TITL 2 FROM THERMUS AQUATICUS IN THE GTP CONFORMATION REMARK 1 REF STRUCTURE V. 1 35 1993 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 5 REMARK 1 AUTH G.POLEKHINA,S.THIRUP,M.KJELDGAARD,P.NISSEN, REMARK 1 AUTH 2 C.LIPPMANN,J.NYBORG REMARK 1 TITL HELIX UNWINDING IN THE EFFECTOR REGION OF REMARK 1 TITL 2 ELONGATION FACTOR EF-TU-GDP REMARK 1 REF STRUCTURE V. 4 1141 1996 REMARK 1 REFN ISSN 0969-2126

REMARK 2 REMARK 2 RESOLUTION. 16.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : O REMARK 3 RECONSTRUCTION SCHEMA : REFERENCE BASED ALIGNMENT REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1EFC/1TTT REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : MANUAL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 2.690 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 16.800 REMARK 3 NUMBER OF PARTICLES : 7985 REMARK 3 CTF CORRECTION METHOD : CTF CORRECTION OF 3D-MAPS REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: SPIDER PACKAGE

REMARK 4 REMARK 4 1LS2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016233.

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 : ASYMMETRIC REMARK 245 NAME OF SAMPLE : E. COLI 70S RIBOSOME-TERNARY REMARK 245 COMPLEX-GDP-KIRROMYCIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID REMARK 245 ETHANE REMARK 245 SAMPLE BUFFER : HEPES-KOH BUFFER AT PH 7.5 REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-MAR-01 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : PHILIPS EM420 REMARK 245 DETECTOR TYPE : KODAK SO163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 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) : 1000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 52000 REMARK 245 SOURCE : LAB6 REMARK 245 ACCELERATION VOLTAGE (KV) : 100 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 SER A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 PHE A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EFC RELATED DB: PDB REMARK 900 1EFC IS INTACT ELONGATION FACTOR FROM E.COLI REMARK 900 RELATED ID: 1TTT RELATED DB: PDB REMARK 900 1TTT IS PHE-TRNA, ELONGATION FACTOR EF-TU: GDPNP TERNARY REMARK 900 COMPLEX REMARK 900 RELATED ID: 1EXM RELATED DB: PDB REMARK 900 1EXM IS THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS REMARK 900 ELONGATION FACTOR TU (EF-TU) IN COMPLEX WITH THE GTP ANALOG REMARK 900 GPPNHP. REMARK 900 RELATED ID: 1LU3 RELATED DB: PDB REMARK 900 1LU3 IS THE SEPARATE FITTING OF THE ANTICODON LOOP REGION REMARK 900 OF TRNA (NUCLEOTIDE 26-42) IN THE LOW RESOLUTION CRYO-EM REMARK 900 MAP OF AN EF-TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND REMARK 900 TO E. COLI 70S RIBOSOME REMARK 900 RELATED ID: EMD-1045 RELATED DB: EMDB

DBREF 1LS2 A 1 393 UNP P0A6N1 EFTU_ECOLI 1 393 DBREF 1LS2 B 1 76 PDB 1LS2 1LS2 1 76

SEQRES 1 B 76 G C G G A U U U A G C U C SEQRES 2 B 76 A G U U G G G A G A G C G SEQRES 3 B 76 C C A G A C U G A A G A U SEQRES 4 B 76 C U G G A G G U C C U G U SEQRES 5 B 76 G U U C G A U C C A C A G SEQRES 6 B 76 A A U U C G C A C C A SEQRES 1 A 393 SER LYS GLU LYS PHE GLU ARG THR LYS PRO HIS VAL ASN SEQRES 2 A 393 VAL GLY THR ILE GLY HIS VAL ASP HIS GLY LYS THR THR SEQRES 3 A 393 LEU THR ALA ALA ILE THR THR VAL LEU ALA LYS THR TYR SEQRES 4 A 393 GLY GLY ALA ALA ARG ALA PHE ASP GLN ILE ASP ASN ALA SEQRES 5 A 393 PRO GLU GLU LYS ALA ARG GLY ILE THR ILE ASN THR SER SEQRES 6 A 393 HIS VAL GLU TYR ASP THR PRO THR ARG HIS TYR ALA HIS SEQRES 7 A 393 VAL ASP CYS PRO GLY HIS ALA ASP TYR VAL LYS ASN MET SEQRES 8 A 393 ILE THR GLY ALA ALA GLN MET ASP GLY ALA ILE LEU VAL SEQRES 9 A 393 VAL ALA ALA THR ASP GLY PRO MET PRO GLN THR ARG GLU SEQRES 10 A 393 HIS ILE LEU LEU GLY ARG GLN VAL GLY VAL PRO TYR ILE SEQRES 11 A 393 ILE VAL PHE LEU ASN LYS CYS ASP MET VAL ASP ASP GLU SEQRES 12 A 393 GLU LEU LEU GLU LEU VAL GLU MET GLU VAL ARG GLU LEU SEQRES 13 A 393 LEU SER GLN TYR ASP PHE PRO GLY ASP ASP THR PRO ILE SEQRES 14 A 393 VAL ARG GLY SER ALA LEU LYS ALA LEU GLU GLY ASP ALA SEQRES 15 A 393 GLU TRP GLU ALA LYS ILE LEU GLU LEU ALA GLY PHE LEU SEQRES 16 A 393 ASP SER TYR ILE PRO GLU PRO GLU ARG ALA ILE ASP LYS SEQRES 17 A 393 PRO PHE LEU LEU PRO ILE GLU ASP VAL PHE SER ILE SER SEQRES 18 A 393 GLY ARG GLY THR VAL VAL THR GLY ARG VAL GLU ARG GLY SEQRES 19 A 393 ILE ILE LYS VAL GLY GLU GLU VAL GLU ILE VAL GLY ILE SEQRES 20 A 393 LYS GLU THR GLN LYS SER THR CYS THR GLY VAL GLU MET SEQRES 21 A 393 PHE ARG LYS LEU LEU ASP GLU GLY ARG ALA GLY GLU ASN SEQRES 22 A 393 VAL GLY VAL LEU LEU ARG GLY ILE LYS ARG GLU GLU ILE SEQRES 23 A 393 GLU ARG GLY GLN VAL LEU ALA LYS PRO GLY THR ILE LYS SEQRES 24 A 393 PRO HIS THR LYS PHE GLU SER GLU VAL TYR ILE LEU SER SEQRES 25 A 393 LYS ASP GLU GLY GLY ARG HIS THR PRO PHE PHE LYS GLY SEQRES 26 A 393 TYR ARG PRO GLN PHE TYR PHE ARG THR THR ASP VAL THR SEQRES 27 A 393 GLY THR ILE GLU LEU PRO GLU GLY VAL GLU MET VAL MET SEQRES 28 A 393 PRO GLY ASP ASN ILE LYS MET VAL VAL THR LEU ILE HIS SEQRES 29 A 393 PRO ILE ALA MET ASP ASP GLY LEU ARG PHE ALA ILE ARG SEQRES 30 A 393 GLU GLY GLY ARG THR VAL GLY ALA GLY VAL VAL ALA LYS SEQRES 31 A 393 VAL LEU SER

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