HEADER RNA BINDING PROTEIN/RNA 18-DEC-06 2OB7 TITLE STRUCTURE OF TMRNA-(SMPB)2 COMPLEX AS INFERRED FROM CRYO-EM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSFER-MESSENGER RNA; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: 16S RIBOSOMAL RNA; COMPND 6 CHAIN: D; COMPND 7 OTHER_DETAILS: HELIX 44 OF 30S RIBOSOMAL SUBUNIT; COMPND 8 MOL_ID: 3; COMPND 9 MOLECULE: SSRA-BINDING PROTEIN; COMPND 10 CHAIN: B, C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 6 ORGANISM_TAXID: 274; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 9 ORGANISM_TAXID: 274 KEYWDS TMRNA, SMPB, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN B, C; P ATOMS ONLY, CHAIN A, D AUTHOR J.FRANK,B.FELDEN,R.GILLET,W.LI REVDAT 5 27-DEC-23 2OB7 1 REMARK REVDAT 4 18-JUL-18 2OB7 1 REMARK REVDAT 3 24-FEB-09 2OB7 1 VERSN REVDAT 2 17-APR-07 2OB7 1 JRNL REVDAT 1 23-JAN-07 2OB7 0 JRNL AUTH R.GILLET,S.KAUR,W.LI,M.HALLIER,B.FELDEN,J.FRANK JRNL TITL SCAFFOLDING AS AN ORGANIZING PRINCIPLE IN TRANS-TRANSLATION. JRNL TITL 2 THE ROLES OF SMALL PROTEIN B AND RIBOSOMAL PROTEIN S1. JRNL REF J.BIOL.CHEM. V. 282 6356 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17179154 JRNL DOI 10.1074/JBC.M609658200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.KAUR,R.GILLET,W.LI,R.GURSKY,J.FRANK REMARK 1 TITL CRYO-EM VISUALIZATION OF TRANSFER MESSENGER RNA WITH TWO REMARK 1 TITL 2 SMPBS IN A STALLED RIBOSOME REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 103 16484 2006 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.VALLE,R.GILLET,K.KAUR,A.HENNE,V.RAMAKRISHNAN,J.FRANK REMARK 1 TITL VISUALIZING TMRNA ENTRY INTO A STALLED RIBOSOME REMARK 1 REF SCIENCE V. 300 127 2003 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. 13.60 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 : 1P6V REMARK 3 REFINEMENT SPACE : REAL 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 FITTING USING STEREO REMARK 3 VISUALIZATION REFINEMENT PROTOCOL--MANUAL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 2.820 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 13.60 REMARK 3 NUMBER OF PARTICLES : 52829 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 2OB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040916. 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 : PRE-ACCOMMODATED RIBOSOMAL REMARK 245 TRANS-TRANSLATION COMPLEX: T. THERMOPHILUS 70S-MRNA-(P-SITE TRNA) REMARK 245 -TMRNA-(SMPB)2-(EF-TU)-GDP-KIRROMYCIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 32.00 REMARK 245 SAMPLE SUPPORT DETAILS : THIS GRID PLUS SAMPLE WAS KEPT REMARK 245 AT -80 DEGREE C FOR SEVERAL REMARK 245 DAYS BEFORE USE. REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 5 SECONDS BEFORE REMARK 245 PLUNGING. RAPID PLUNGE FREEZING REMARK 245 IN LIQUID ETHANE. REMARK 245 SAMPLE BUFFER : POLIMIX REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : SEE EXPERIMENTAL PROCEDURES IN REMARK 245 KAUR ET AL. (PNAS). [DEPOSITION REFERS TO STRUCTURE OF TMRNA- REMARK 245 (SMPB)2 COMPLEX DERIVED BY FITTING OF EM MAP FROM KAUR ET AL. REMARK 245 FITTING WAS MODIFIED IN GILLET ET AL.] REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 01-JUN-04 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 296.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1475.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3635.00 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) : 1500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 55000 REMARK 245 CALIBRATED MAGNIFICATION : 49000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, B, C 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 GLY B 1 REMARK 465 LYS B 2 REMARK 465 LYS B 70 REMARK 465 HIS B 71 REMARK 465 ALA B 72 REMARK 465 THR B 73 REMARK 465 ILE B 74 REMARK 465 GLU B 75 REMARK 465 TYR B 131 REMARK 465 ASP B 132 REMARK 465 ARG B 133 REMARK 465 ARG B 134 REMARK 465 ARG B 135 REMARK 465 GLU B 136 REMARK 465 LEU B 137 REMARK 465 LYS B 138 REMARK 465 GLU B 139 REMARK 465 LYS B 140 REMARK 465 ALA B 141 REMARK 465 MET B 142 REMARK 465 LYS B 143 REMARK 465 ARG B 144 REMARK 465 GLU B 145 REMARK 465 LEU B 146 REMARK 465 GLU B 147 REMARK 465 ARG B 148 REMARK 465 GLU B 149 REMARK 465 PHE B 150 REMARK 465 LYS B 151 REMARK 465 GLY B 152 REMARK 465 LYS B 153 REMARK 465 ILE B 154 REMARK 465 HIS B 155 REMARK 465 LEU B 156 REMARK 465 GLY C 1 REMARK 465 LYS C 2 REMARK 465 THR C 73 REMARK 465 ILE C 74 REMARK 465 GLU C 75 REMARK 465 LYS C 102 REMARK 465 GLY C 103 REMARK 465 TYR C 104 REMARK 465 THR C 105 REMARK 465 ALA C 125 REMARK 465 LYS C 126 REMARK 465 GLY C 127 REMARK 465 LYS C 128 REMARK 465 LYS C 129 REMARK 465 LEU C 130 REMARK 465 TYR C 131 REMARK 465 ASP C 132 REMARK 465 ARG C 133 REMARK 465 ARG C 134 REMARK 465 ARG C 135 REMARK 465 GLU C 136 REMARK 465 LEU C 137 REMARK 465 LYS C 138 REMARK 465 GLU C 139 REMARK 465 LYS C 140 REMARK 465 ALA C 141 REMARK 465 MET C 142 REMARK 465 LYS C 143 REMARK 465 ARG C 144 REMARK 465 GLU C 145 REMARK 465 LEU C 146 REMARK 465 GLU C 147 REMARK 465 ARG C 148 REMARK 465 GLU C 149 REMARK 465 PHE C 150 REMARK 465 LYS C 151 REMARK 465 GLY C 152 REMARK 465 LYS C 153 REMARK 465 ILE C 154 REMARK 465 HIS C 155 REMARK 465 LEU C 156 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 P A A 101 P C A 138 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PV6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COMPLEX FORMED BY SMPB AND TLD OF TMRNA. REMARK 900 RELATED ID: 1N34 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF 30S SUBUNIT FROM T. THERMOPHILUS (ONLY HELIX 44 REMARK 900 DEPOSITED HERE, FOR POSITIONAL REFERENCE) REMARK 900 RELATED ID: EMD-1310 RELATED DB: EMDB REMARK 900 STALLED 70S RIBOSOME (I.E., WITHOUT ANY CODON IN A SITE) BOUND WITH REMARK 900 SMPB REMARK 900 RELATED ID: EMD-1311 RELATED DB: EMDB REMARK 900 PRE-ACCOMMODATED RIBOSOMAL TRANS-TRANSLATION COMPLEX: T. REMARK 900 THERMOPHILUS 70S-MRNA-(P-SITE TRNA)-TMRNA-(SMPB)2-(EF-TU)-GDP- REMARK 900 KIRROMYCIN IN THE PRESENCE OF PROTEIN S1 REMARK 900 RELATED ID: EMD-1312 RELATED DB: EMDB REMARK 900 PRE-ACCOMMODATED RIBOSOMAL TRANS-TRANSLATION COMPLEX: T. REMARK 900 THERMOPHILUS 70S-MRNA-(P-SITE TRNA)-TMRNA-(SMPB)2-(EF-TU)-GDP- REMARK 900 KIRROMYCIN IN THE ABSENCE OF PROTEIN S1 REMARK 900 RELATED ID: 1Q2B RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF EF-TU FITTED INTO PRE-ACCOMMODATED RIBOSOMAL REMARK 900 TRANSLATION COMPLEX, PLACED IN THE RIBOSOMAL ENRIVONMENT BY REMARK 900 REFERENCE TO S12 AND HELIX 44 OF THE SMALL SUBUNIT, AND HELIX 69 REMARK 900 AND GAC OF THE LARGE SUBUNIT (1QZC) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DEPOSITED ENTRY IS A MODEL TO FIT THE CRYO-EM REMARK 999 MAP OF TMRNA+SMPB(2) FROM THERMUS THERMOPHILUS. REMARK 999 THE DEPOSITION INCLUDES 4 CHAINS: REMARK 999 CHAIN A: TMRNA MODEL REMARK 999 CHAINS B,C: SMPB (FROM 1P6V.PDB CHAIN A, FOR SMPB REMARK 999 FROM AQUIFEX AEOLICUS); REMARK 999 CHAIN D: HELIX 44 OF 30S RIBOSOMAL SUBUNIT REMARK 999 (FROM 1N34.PDB CHAIN A:1406-1496. X-RAY STRUCTURE REMARK 999 OF 1N34 IS FROM THERMUS THERMOPHILUS). REMARK 999 THE E.COLI MODEL ESCHCOLITM3D-MODEL-72.PDB REMARK 999 (HTTP://WWW.AG.AUBURN.EDU/MIRROR/TMRDB/RNA/TMRNA.HTML/) REMARK 999 WAS USED AS A TEMPLATE TO BUILD THE MODEL BY REPLACING REMARK 999 SEVERAL FRAGMENTS WHICH HAVE X-RAY CRYSTAL AS ALTERNATIVES, REMARK 999 AND BY FITTING ALL THE STRUCTURES INTO THE CRYO-EM MAPS. REMARK 999 NUCLEOTIDE NUMBERING IN THIS MODEL FOLLOWS E.COLI SEQUENCE. REMARK 999 CONSIDERING THE DIFFERENCES BETWEEN TMRNA SEQUENCES FROM REMARK 999 E.COLI AND T.THERMOPHILUS, A SMALL NUMBER OF NUCLEOTIDES REMARK 999 IN THE TEMPLATE MODEL ARE NOT INCLUDED IN THIS MODEL. DBREF 2OB7 A 1 362 PDB 2OB7 2OB7 1 362 DBREF 2OB7 D 1406 1496 PDB 2OB7 2OB7 1406 1496 DBREF 2OB7 B 1 156 PDB 2OB7 2OB7 1 156 DBREF 2OB7 C 1 156 PDB 2OB7 2OB7 1 156 SEQRES 1 A 328 G G C G C G U A U U C G A SEQRES 2 A 328 C G G G G A C C C A A G G SEQRES 3 A 328 U G C A U G C C G A G G G SEQRES 4 A 328 G C G G U U G G C C U C G SEQRES 5 A 328 U A A A A A G C C G C A A SEQRES 6 A 328 C G G C A U A A C U G C C SEQRES 7 A 328 A A C A C C A A C U A C G SEQRES 8 A 328 C U C U G G C A G C U U A SEQRES 9 A 328 A U A A C C U G C U U A C SEQRES 10 A 328 C U C U C U C C C U A G C SEQRES 11 A 328 C U C C G C U C U U A G G SEQRES 12 A 328 A C G G G G A U C A A G A SEQRES 13 A 328 G A G G U C A A A C C C A SEQRES 14 A 328 A A A G A G A U C G C G U SEQRES 15 A 328 G G A A G C C C U G C C U SEQRES 16 A 328 G G G G U U G A A G C G U SEQRES 17 A 328 U A A A A C U U A A U C A SEQRES 18 A 328 G G C U G U U U G U U A G SEQRES 19 A 328 U G G C G U G U C C G U C SEQRES 20 A 328 C G C A G C U G G C A A G SEQRES 21 A 328 C G A A U G U A A A G A C SEQRES 22 A 328 U G A C U A A G C A U G A SEQRES 23 A 328 C C G A G G A C C U C G G SEQRES 24 A 328 A C G C G G G U U C G A U SEQRES 25 A 328 U C C C G C A C G C G C C SEQRES 26 A 328 U C C SEQRES 1 D 86 U C A C G C C A U G G G A SEQRES 2 D 86 G C G G G C U C U A C C C SEQRES 3 D 86 G A A G U C G C C G G G A SEQRES 4 D 86 G C C U A C G G G C A G G SEQRES 5 D 86 C G C C G A G G G U A G G SEQRES 6 D 86 G C C C G U G A C U G G G SEQRES 7 D 86 G C G A A G U C SEQRES 1 B 156 GLY LYS SER ASP LYS ILE ILE PRO ILE ALA GLU ASN LYS SEQRES 2 B 156 GLU ALA LYS ALA LYS TYR ASP ILE LEU GLU THR TYR GLU SEQRES 3 B 156 ALA GLY ILE VAL LEU LYS GLY SER GLU VAL LYS SER LEU SEQRES 4 B 156 ARG GLU LYS GLY THR VAL SER PHE LYS ASP SER PHE VAL SEQRES 5 B 156 ARG ILE GLU ASN GLY GLU ALA TRP LEU TYR ASN LEU TYR SEQRES 6 B 156 ILE ALA PRO TYR LYS HIS ALA THR ILE GLU ASN HIS ASP SEQRES 7 B 156 PRO LEU ARG LYS ARG LYS LEU LEU LEU HIS LYS ARG GLU SEQRES 8 B 156 ILE MET ARG LEU TYR GLY LYS VAL GLN GLU LYS GLY TYR SEQRES 9 B 156 THR ILE ILE PRO LEU LYS LEU TYR TRP LYS ASN ASN LYS SEQRES 10 B 156 VAL LYS VAL LEU ILE ALA LEU ALA LYS GLY LYS LYS LEU SEQRES 11 B 156 TYR ASP ARG ARG ARG GLU LEU LYS GLU LYS ALA MET LYS SEQRES 12 B 156 ARG GLU LEU GLU ARG GLU PHE LYS GLY LYS ILE HIS LEU SEQRES 1 C 156 GLY LYS SER ASP LYS ILE ILE PRO ILE ALA GLU ASN LYS SEQRES 2 C 156 GLU ALA LYS ALA LYS TYR ASP ILE LEU GLU THR TYR GLU SEQRES 3 C 156 ALA GLY ILE VAL LEU LYS GLY SER GLU VAL LYS SER LEU SEQRES 4 C 156 ARG GLU LYS GLY THR VAL SER PHE LYS ASP SER PHE VAL SEQRES 5 C 156 ARG ILE GLU ASN GLY GLU ALA TRP LEU TYR ASN LEU TYR SEQRES 6 C 156 ILE ALA PRO TYR LYS HIS ALA THR ILE GLU ASN HIS ASP SEQRES 7 C 156 PRO LEU ARG LYS ARG LYS LEU LEU LEU HIS LYS ARG GLU SEQRES 8 C 156 ILE MET ARG LEU TYR GLY LYS VAL GLN GLU LYS GLY TYR SEQRES 9 C 156 THR ILE ILE PRO LEU LYS LEU TYR TRP LYS ASN ASN LYS SEQRES 10 C 156 VAL LYS VAL LEU ILE ALA LEU ALA LYS GLY LYS LYS LEU SEQRES 11 C 156 TYR ASP ARG ARG ARG GLU LEU LYS GLU LYS ALA MET LYS SEQRES 12 C 156 ARG GLU LEU GLU ARG GLU PHE LYS GLY LYS ILE HIS LEU 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