PDB Short entry for 2VAZ HEADER TRANSLATION 05-SEP-07 2VAZ TITLE MODEL OF THE S15-MRNA COMPLEX FITTED INTO THE CRYO-EM MAP OF THE 70S TITLE 2 ENTRAPMENT COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RPSO MRNA OPERATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HAIRPIN LOOP DOMAIN I AND PSEUDOKNOT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 30S RIBOSOMAL PROTEIN S15; COMPND 8 CHAIN: F; COMPND 9 SYNONYM: REPRESSOR S15; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS TRANSLATION, PLATFORM-BINDING CENTER, GENE EXPRESSION REGULATION, KEYWDS 2 RIBOSOMAL PROTEIN, RIBONUCLEOPROTEIN, PROTEIN SYNTHESIS, TRANSLATION KEYWDS 3 INITIATION, RIBOSOME, RIBOSWITCH, RNA-BINDING, RRNA-BINDING, RNA KEYWDS 4 PSEUDOKNOT, MRNA STRUCTURE, REPRESSOR PROTEIN EXPDTA ELECTRON MICROSCOPY MDLTYP P ATOMS ONLY, CHAIN A ; CA ATOMS ONLY, CHAIN F AUTHOR S.MARZI,A.G.MYASNIKOV,A.SERGANOV,C.EHRESMANN,P.ROMBY,M.YUSUPOV, AUTHOR 2 B.P.KLAHOLZ REVDAT 4 02-AUG-17 2VAZ 1 REVDAT 3 14-NOV-12 2VAZ 1 REMARK VERSN REVDAT 2 24-FEB-09 2VAZ 1 VERSN REVDAT 1 02-OCT-07 2VAZ 0 JRNL AUTH S.MARZI,A.G.MYASNIKOV,A.SERGANOV,C.EHRESMANN,P.ROMBY, JRNL AUTH 2 M.YUSUPOV,B.P.KLAHOLZ JRNL TITL STRUCTURED MRNAS REGULATE TRANSLATION INITIATION BY BINDING JRNL TITL 2 TO THE PLATFORM OF THE RIBOSOME. JRNL REF CELL(CAMBRIDGE,MASS.) V. 130 1019 2007 JRNL REFN ISSN 0092-8674 JRNL PMID 17889647 JRNL DOI 10.1016/J.CELL.2007.07.008 REMARK 2 REMARK 2 RESOLUTION. 10.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : O, PYMOL, IMAGIC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2AW7 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 REFINEMENT PROTOCOL--X-RAY AND REMARK 3 HOMOLOGY MODELS REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 3.000 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 10.00 REMARK 3 NUMBER OF PARTICLES : 31415 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM REMARK 3 ELECTRON MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 3 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 3 THESE RECORDS ARE MEANINGLESS. THE MRNA HAS BEEN MODELED USING REMARK 3 MANIP (MASSIRE AND WESTHOF). REMARK 4 REMARK 4 2VAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1290033682. 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 : 70S PRE-INITIATION COMPLEX REMARK 245 ENTRAPPED BY S15- RPSOMRNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FOR 2 SECONDS BEFORE REMARK 245 PLUNGING IN LIQUID ETHANE USING REMARK 245 A HOME-MADE CRYO- PLUNGER REMARK 245 SAMPLE BUFFER : 20 MM TRIS-HCL PH 7.5, 60 MM REMARK 245 KCL, 1MM DTT, 7.5 MM MGCL2 REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 05-JAN-05 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 77.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 20.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 51484 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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 G A -15 REMARK 465 G A -14 REMARK 465 G A -13 REMARK 465 C A -12 REMARK 465 G A -11 REMARK 465 A A -10 REMARK 465 A A -9 REMARK 465 U A -8 REMARK 465 U A -7 REMARK 465 C A -6 REMARK 465 G A -5 REMARK 465 A A -4 REMARK 465 G A -3 REMARK 465 C A -2 REMARK 465 U A -1 REMARK 465 C A 0 REMARK 465 G A 1 REMARK 465 G A 2 REMARK 465 U A 3 REMARK 465 A A 4 REMARK 465 C A 5 REMARK 465 C A 6 REMARK 465 C A 7 REMARK 465 A A 8 REMARK 465 C A 76 REMARK 465 U A 77 REMARK 465 U A 78 REMARK 465 U A 79 REMARK 465 C A 80 REMARK 465 A A 81 REMARK 465 U A 82 REMARK 465 U A 83 REMARK 465 C A 84 REMARK 465 U A 85 REMARK 465 A A 86 REMARK 465 U A 87 REMARK 465 A A 88 REMARK 465 U A 89 REMARK 465 A A 90 REMARK 465 C A 91 REMARK 465 U A 101 REMARK 465 A A 102 REMARK 465 A A 103 REMARK 465 A A 104 REMARK 465 A A 105 REMARK 465 U A 106 REMARK 465 G A 107 REMARK 465 U A 108 REMARK 465 G A 115 REMARK 465 U A 116 REMARK 465 A A 117 REMARK 465 C A 118 REMARK 465 U A 119 REMARK 465 G A 120 REMARK 465 A A 121 REMARK 465 A A 122 REMARK 465 G A 123 REMARK 465 C A 124 REMARK 465 A A 125 REMARK 465 A A 126 REMARK 465 C A 127 REMARK 465 A A 128 REMARK 465 G A 129 REMARK 465 C A 130 REMARK 465 U A 131 REMARK 465 A A 132 REMARK 465 A A 133 REMARK 465 A A 134 REMARK 465 A A 135 REMARK 465 U A 136 REMARK 465 C A 137 REMARK 465 G A 138 REMARK 465 U A 139 REMARK 465 U A 140 REMARK 465 U A 141 REMARK 465 C A 142 REMARK 465 U A 143 REMARK 465 G A 144 REMARK 465 A A 145 REMARK 465 G A 146 REMARK 465 U A 147 REMARK 465 U A 148 REMARK 465 U A 149 REMARK 465 G A 150 REMARK 465 G A 151 REMARK 465 U A 152 REMARK 465 C A 153 REMARK 465 G A 154 REMARK 465 A A 155 REMARK 465 C A 156 REMARK 465 C A 157 REMARK 465 U A 158 REMARK 465 G A 159 REMARK 465 C A 160 REMARK 465 A A 161 REMARK 465 G A 162 REMARK 465 G A 163 REMARK 465 C A 164 REMARK 465 A A 165 REMARK 465 U A 166 REMARK 465 G A 167 REMARK 465 C A 168 REMARK 465 A A 169 REMARK 465 MET F 100 REMARK 465 ARG F 187 REMARK 465 ARG F 188 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1391 RELATED DB: EMDB REMARK 900 STRUCTURED MRNAS REGULATE TRANSLATION INITIATION BY BINDING TO A REMARK 900 DEDICATED SITE ON THE RIBOSOME. REMARK 900 RELATED ID: 1P6G RELATED DB: PDB REMARK 900 REAL SPACE REFINED COORDINATES OF THE 30S SUBUNIT FITTEDINTO THE REMARK 900 LOW RESOLUTION CRYO- EM MAP OF THE EF-G.GTP STATE OF E. COLI 70S REMARK 900 RIBOSOME REMARK 900 RELATED ID: 1P87 RELATED DB: PDB REMARK 900 REAL SPACE REFINED COORDINATES OF THE 30S SUBUNIT FITTEDINTO THE REMARK 900 LOW RESOLUTION CRYO- EM MAP OF THE INITIATION-LIKESTATE OF E. COLI REMARK 900 70S RIBOSOME REMARK 900 RELATED ID: 2AVY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROMESCHERICHIA COLI AT REMARK 900 3.5 A RESOLUTION. THIS FILE CONTAINS THE 30S SUBUNIT OF ONE 70S REMARK 900 RIBOSOME. THE ENTIRE CRYSTALSTRUCTURE CONTAINS TWO 70S RIBOSOMES REMARK 900 AND IS DESCRIBED INREMARK 400. REMARK 900 RELATED ID: 2AW7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOME FROMESCHERICHIA COLI AT REMARK 900 3.5 A RESOLUTION. THIS FILE CONTAINS THE 30S SUBUNIT OF THE SECOND REMARK 900 70S RIBOSOME. THE ENTIRECRYSTAL STRUCTURE CONTAINS TWO 70S REMARK 900 RIBOSOMES AND ISDESCRIBED IN REMARK 400. DBREF 2VAZ A -15 169 PDB 2VAZ 2VAZ -15 169 DBREF 2VAZ F 100 100 PDB 2VAZ 2VAZ 100 100 DBREF 2VAZ F 101 188 UNP P0ADZ4 RS15_ECOLI 1 88 SEQRES 1 A 185 G G G C G A A U U C G A G SEQRES 2 A 185 C U C G G U A C C C A A C SEQRES 3 A 185 G U C G C G U A A A U U G SEQRES 4 A 185 U U U A A C A C U U U G C SEQRES 5 A 185 G U A A C G U A C A C U G SEQRES 6 A 185 G G A U C G C U G A A U U SEQRES 7 A 185 A G A G A U C G G C G U C SEQRES 8 A 185 C U U U C A U U C U A U A SEQRES 9 A 185 U A C U A A G G A G G U U SEQRES 10 A 185 A A A A U G U C U C U A A SEQRES 11 A 185 G U A C U G A A G C A A C SEQRES 12 A 185 A G C U A A A A U C G U U SEQRES 13 A 185 U C U G A G U U U G G U C SEQRES 14 A 185 G A C C U G C A G G C A U SEQRES 15 A 185 G C A SEQRES 1 F 89 MET SER LEU SER THR GLU ALA THR ALA LYS ILE VAL SER SEQRES 2 F 89 GLU PHE GLY ARG ASP ALA ASN ASP THR GLY SER THR GLU SEQRES 3 F 89 VAL GLN VAL ALA LEU LEU THR ALA GLN ILE ASN HIS LEU SEQRES 4 F 89 GLN GLY HIS PHE ALA GLU HIS LYS LYS ASP HIS HIS SER SEQRES 5 F 89 ARG ARG GLY LEU LEU ARG MET VAL SER GLN ARG ARG LYS SEQRES 6 F 89 LEU LEU ASP TYR LEU LYS ARG LYS ASP VAL ALA ARG TYR SEQRES 7 F 89 THR GLN LEU ILE GLU ARG LEU GLY LEU ARG ARG 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