HEADER RNA 21-MAY-02 1LU3 TITLE SEPARATE FITTING OF THE ANTICODON LOOP REGION OF TRNA (NUCLEOTIDE 26- TITLE 2 42) IN THE LOW RESOLUTION CRYO-EM MAP OF AN EF-TU TERNARY COMPLEX TITLE 3 (GDP AND KIRROMYCIN) BOUND TO E. COLI 70S RIBOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHENYLALANINE TRANSFER RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ANTICODON LOOP REGION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS TRNA, TERNARY COMPLEX, CRYO-EM, 70S E.COLI RIBOSOME, CONFORMATIONAL KEYWDS 2 CHANGE, RNA EXPDTA ELECTRON MICROSCOPY AUTHOR M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI,N.BURKHARDT,K.H.NIERHAUS, AUTHOR 2 R.K.AGRAWAL,J.FRANK REVDAT 4 18-JUL-18 1LU3 1 REMARK REVDAT 3 24-FEB-09 1LU3 1 VERSN REVDAT 2 01-APR-03 1LU3 1 JRNL REVDAT 1 26-JUN-02 1LU3 0 JRNL AUTH M.VALLE,J.SENGUPTA,N.K.SWAMI,R.A.GRASSUCCI,N.BURKHARDT, JRNL AUTH 2 K.H.NIERHAUS,R.K.AGRAWAL,J.FRANK JRNL TITL CRYO-EM REVEALS AN ACTIVE ROLE FOR AMINOACYL-TRNA IN THE JRNL TITL 2 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 EF-TU FROM REMARK 1 TITL 2 E.COLI IN GDP CONFORMATION AT 2.05A 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,L.RESHETNIKOVA, REMARK 1 AUTH 2 B.F.C.CLARK,J.NYBORG REMARK 1 TITL CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF THE PHE-TRNAPHE, REMARK 1 TITL 2 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 E.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 FROM REMARK 1 TITL 2 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,C.LIPPMANN, REMARK 1 AUTH 2 J.NYBORG REMARK 1 TITL HELIX UNWINDING IN THE EFFECTOR REGION OF ELONGATION FACTOR REMARK 1 TITL 2 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, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1TTT REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--MANUAL 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) : 16.80 REMARK 3 NUMBER OF PARTICLES : 7985 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: SPIDER PACKAGE REMARK 4 REMARK 4 1LU3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016269. 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 : 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 ETHANE REMARK 245 SAMPLE BUFFER : HEPES-KOH BUFFER AT PH 7.5 REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : E.COLI 70S RIBOSOME-TERNARY REMARK 245 COMPLEX-GDP-KIRROMYCIN 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 : FEI/PHILIPS EM420 REMARK 245 DETECTOR TYPE : KODAK SO-163 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) : 10.00 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 26 N3 G A 26 C4 0.090 REMARK 500 G A 26 C4 G A 26 C5 -0.047 REMARK 500 G A 26 C5 G A 26 N7 0.049 REMARK 500 G A 26 N7 G A 26 C8 -0.043 REMARK 500 G A 26 C8 G A 26 N9 -0.071 REMARK 500 G A 26 N9 G A 26 C4 -0.066 REMARK 500 C A 27 C2 C A 27 N3 0.092 REMARK 500 C A 27 N3 C A 27 C4 -0.064 REMARK 500 C A 27 C4 C A 27 C5 0.050 REMARK 500 C A 28 C2 C A 28 N3 0.090 REMARK 500 C A 28 N3 C A 28 C4 -0.065 REMARK 500 C A 28 C4 C A 28 C5 0.050 REMARK 500 A A 29 C5 A A 29 N7 -0.048 REMARK 500 A A 29 N7 A A 29 C8 -0.044 REMARK 500 A A 29 C8 A A 29 N9 -0.067 REMARK 500 G A 30 N3 G A 30 C4 0.090 REMARK 500 G A 30 C4 G A 30 C5 -0.047 REMARK 500 G A 30 C5 G A 30 N7 0.048 REMARK 500 G A 30 N7 G A 30 C8 -0.043 REMARK 500 G A 30 C8 G A 30 N9 -0.071 REMARK 500 G A 30 N9 G A 30 C4 -0.066 REMARK 500 A A 31 C5 A A 31 N7 -0.048 REMARK 500 A A 31 N7 A A 31 C8 -0.043 REMARK 500 A A 31 C8 A A 31 N9 -0.065 REMARK 500 C A 32 C2 C A 32 N3 0.092 REMARK 500 C A 32 N3 C A 32 C4 -0.065 REMARK 500 C A 32 C4 C A 32 C5 0.050 REMARK 500 G A 34 N3 G A 34 C4 0.091 REMARK 500 G A 34 C4 G A 34 C5 -0.048 REMARK 500 G A 34 C5 G A 34 N7 0.047 REMARK 500 G A 34 N7 G A 34 C8 -0.043 REMARK 500 G A 34 C8 G A 34 N9 -0.072 REMARK 500 G A 34 N9 G A 34 C4 -0.065 REMARK 500 A A 35 C5 A A 35 N7 -0.050 REMARK 500 A A 35 N7 A A 35 C8 -0.044 REMARK 500 A A 35 C8 A A 35 N9 -0.066 REMARK 500 A A 36 C5 A A 36 N7 -0.050 REMARK 500 A A 36 N7 A A 36 C8 -0.043 REMARK 500 A A 36 C8 A A 36 N9 -0.065 REMARK 500 G A 37 C2 G A 37 N3 -0.050 REMARK 500 G A 37 N3 G A 37 C4 0.089 REMARK 500 G A 37 C4 G A 37 C5 -0.047 REMARK 500 G A 37 C5 G A 37 N7 0.048 REMARK 500 G A 37 N7 G A 37 C8 -0.044 REMARK 500 G A 37 C8 G A 37 N9 -0.072 REMARK 500 G A 37 N9 G A 37 C4 -0.065 REMARK 500 A A 38 C5 A A 38 N7 -0.048 REMARK 500 A A 38 N7 A A 38 C8 -0.042 REMARK 500 A A 38 C8 A A 38 N9 -0.065 REMARK 500 C A 40 C2 C A 40 N3 0.092 REMARK 500 REMARK 500 THIS ENTRY HAS 58 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 G A 26 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 G A 26 C2 - N3 - C4 ANGL. DEV. = 8.3 DEGREES REMARK 500 G A 26 N3 - C4 - C5 ANGL. DEV. = -9.5 DEGREES REMARK 500 G A 26 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 G A 26 C4 - C5 - N7 ANGL. DEV. = -9.6 DEGREES REMARK 500 G A 26 C5 - N7 - C8 ANGL. DEV. = 5.2 DEGREES REMARK 500 G A 26 N7 - C8 - N9 ANGL. DEV. = -3.5 DEGREES REMARK 500 G A 26 N9 - C4 - C5 ANGL. DEV. = 5.9 DEGREES REMARK 500 G A 26 C6 - C5 - N7 ANGL. DEV. = 7.9 DEGREES REMARK 500 G A 26 N1 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 26 C5 - C6 - O6 ANGL. DEV. = -7.9 DEGREES REMARK 500 C A 27 OP1 - P - OP2 ANGL. DEV. = -10.4 DEGREES REMARK 500 C A 27 N3 - C4 - C5 ANGL. DEV. = -4.2 DEGREES REMARK 500 C A 27 C4 - C5 - C6 ANGL. DEV. = 3.1 DEGREES REMARK 500 C A 27 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 C A 27 N3 - C4 - N4 ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 28 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 C A 28 N3 - C4 - C5 ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 28 C4 - C5 - C6 ANGL. DEV. = 3.0 DEGREES REMARK 500 C A 28 N3 - C4 - N4 ANGL. DEV. = 5.0 DEGREES REMARK 500 A A 29 OP1 - P - OP2 ANGL. DEV. = -10.2 DEGREES REMARK 500 A A 29 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES REMARK 500 A A 29 C2 - N3 - C4 ANGL. DEV. = 7.2 DEGREES REMARK 500 A A 29 N3 - C4 - C5 ANGL. DEV. = -6.9 DEGREES REMARK 500 A A 29 C4 - C5 - C6 ANGL. DEV. = 5.3 DEGREES REMARK 500 A A 29 C4 - C5 - N7 ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 29 C5 - N7 - C8 ANGL. DEV. = 6.0 DEGREES REMARK 500 A A 29 N3 - C4 - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 A A 29 N1 - C6 - N6 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 30 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 G A 30 C2 - N3 - C4 ANGL. DEV. = 8.4 DEGREES REMARK 500 G A 30 N3 - C4 - C5 ANGL. DEV. = -9.7 DEGREES REMARK 500 G A 30 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 30 C4 - C5 - N7 ANGL. DEV. = -9.5 DEGREES REMARK 500 G A 30 C5 - N7 - C8 ANGL. DEV. = 5.1 DEGREES REMARK 500 G A 30 N7 - C8 - N9 ANGL. DEV. = -3.5 DEGREES REMARK 500 G A 30 N9 - C4 - C5 ANGL. DEV. = 5.9 DEGREES REMARK 500 G A 30 N3 - C4 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 30 C6 - C5 - N7 ANGL. DEV. = 7.7 DEGREES REMARK 500 G A 30 N1 - C6 - O6 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 30 C5 - C6 - O6 ANGL. DEV. = -8.1 DEGREES REMARK 500 A A 31 OP1 - P - OP2 ANGL. DEV. = -10.1 DEGREES REMARK 500 A A 31 N1 - C2 - N3 ANGL. DEV. = -6.6 DEGREES REMARK 500 A A 31 C2 - N3 - C4 ANGL. DEV. = 7.2 DEGREES REMARK 500 A A 31 N3 - C4 - C5 ANGL. DEV. = -6.9 DEGREES REMARK 500 A A 31 C4 - C5 - C6 ANGL. DEV. = 5.3 DEGREES REMARK 500 A A 31 C4 - C5 - N7 ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 31 C5 - N7 - C8 ANGL. DEV. = 6.0 DEGREES REMARK 500 A A 31 N3 - C4 - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 A A 31 N1 - C6 - N6 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 129 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LS2 RELATED DB: PDB REMARK 900 1LS2 IS FITTING OF EF-TU AND TRNA IN THE LOW RESOLUTION CRYO-EM MAP REMARK 900 OF AN EF-TU TERNARY COMPLEX (GDP AND KIRROMYCIN) BOUND TO E.COLI REMARK 900 70S RIBOSOME 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 COMPLEX REMARK 900 RELATED ID: 1EXM RELATED DB: PDB REMARK 900 1EXM IS CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS ELONGATION FACTOR REMARK 900 TU(EF-TU) IN COMPLEX WITH THE GTP ANALOG GPPNHP REMARK 900 RELATED ID: EMD-1045 RELATED DB: EMDB DBREF 1LU3 A 26 42 PDB 1LU3 1LU3 26 42 SEQRES 1 A 17 G C C A G A C U G A A G A SEQRES 2 A 17 PSU C U G MODRES 1LU3 PSU A 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET PSU A 39 20 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE FORMUL 1 PSU C9 H13 N2 O9 P LINK O3' A A 38 P PSU A 39 1555 1555 1.60 LINK O3' PSU A 39 P C A 40 1555 1555 1.60 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 MASTER 281 0 1 0 0 0 0 6 0 0 0 2 END