HEADER RIBOSOMAL PROTEIN/RNA 22-AUG-07 2R1G TITLE COORDINATES OF THE THERMUS THERMOPHILUS 30S COMPONENTS NEIGHBORING TITLE 2 RBFA AS OBTAINED BY FITTING INTO THE CRYO-EM MAP OF A 30S-RBFA TITLE 3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 16S RIBOSOMAL RNA HELIX 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 16S RIBOSOMAL RNA HELIX 18; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 16S RIBOSOMAL RNA HELIX 27; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: 16S RIBOSOMAL RNA HELIX 28; COMPND 15 CHAIN: D; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: 16S RIBOSOMAL RNA HELIX 44; COMPND 19 CHAIN: E; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: 16S RIBOSOMAL RNA HELIX 44; COMPND 23 CHAIN: X; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: 16S RIBOSOMAL RNA HELIX 45; COMPND 27 CHAIN: F; COMPND 28 ENGINEERED: YES; COMPND 29 MOL_ID: 8; COMPND 30 MOLECULE: 30S RIBOSOMAL PROTEIN S9; COMPND 31 CHAIN: G; COMPND 32 ENGINEERED: YES; COMPND 33 MOL_ID: 9; COMPND 34 MOLECULE: 30S RIBOSOMAL PROTEIN S12; COMPND 35 CHAIN: H; COMPND 36 FRAGMENT: RESIDUES 5-128; COMPND 37 ENGINEERED: YES; COMPND 38 MOL_ID: 10; COMPND 39 MOLECULE: 30S RIBOSOMAL PROTEIN S13; COMPND 40 CHAIN: I; COMPND 41 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 5; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630; SOURCE 21 MOL_ID: 6; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 MOL_ID: 7; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 28 ORGANISM_TAXID: 32630; SOURCE 29 MOL_ID: 8; SOURCE 30 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 31 ORGANISM_TAXID: 262724; SOURCE 32 STRAIN: HB27; SOURCE 33 GENE: RPSI, RPS9; SOURCE 34 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 35 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 36 MOL_ID: 9; SOURCE 37 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 38 ORGANISM_TAXID: 262724; SOURCE 39 STRAIN: HB27; SOURCE 40 GENE: RPSL, RPS12; SOURCE 41 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 42 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 43 MOL_ID: 10; SOURCE 44 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 45 ORGANISM_TAXID: 262724; SOURCE 46 STRAIN: HB27; SOURCE 47 GENE: RPSM, RPS13; SOURCE 48 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 49 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 30S RIBOSOME MATURATION PROTEIN RBFA, COLD SHOCK RESPONSE PROTEIN KEYWDS 2 RBFA, 30S-RBFA COMPLEX, RBFA BINDING SITE ON THE 30S, KEYWDS 3 RIBONUCLEOPROTEIN, RIBOSOMAL PROTEIN, RNA-BINDING, RRNA-BINDING, KEYWDS 4 TRNA-BINDING, ANTIBIOTIC RESISTANCE, RIBOSOMAL PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN G, H, I; P ATOMS ONLY, CHAIN A, B, C, D, E, X, F AUTHOR P.P.DATTA,D.N.WILSON,M.KAWAZOE,N.K.SWAMI,T.KAMINISHI,M.R.SHARMA, AUTHOR 2 T.M.BOOTH,C.TAKEMOTO,P.FUCINI,S.YOKOYAMA,R.K.AGRAWAL REVDAT 6 13-MAR-24 2R1G 1 REMARK REVDAT 5 18-DEC-19 2R1G 1 SOURCE REMARK REVDAT 4 13-JUL-11 2R1G 1 VERSN REVDAT 3 02-FEB-10 2R1G 1 REMARK REVDAT 2 24-FEB-09 2R1G 1 VERSN REVDAT 1 18-MAR-08 2R1G 0 JRNL AUTH P.P.DATTA,D.N.WILSON,M.KAWAZOE,N.K.SWAMI,T.KAMINISHI, JRNL AUTH 2 M.R.SHARMA,T.M.BOOTH,C.TAKEMOTO,P.FUCINI,S.YOKOYAMA, JRNL AUTH 3 R.K.AGRAWAL JRNL TITL STRUCTURAL ASPECTS OF RBFA ACTION DURING SMALL RIBOSOMAL JRNL TITL 2 SUBUNIT ASSEMBLY. JRNL REF MOL.CELL V. 28 434 2007 JRNL REFN ISSN 1097-2765 JRNL PMID 17996707 JRNL DOI 10.1016/J.MOLCEL.2007.08.026 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.T.WIMBERLY,D.E.BRODERSEN,W.M.CLEMONS,R.J.MORGAN-WARREN, REMARK 1 AUTH 2 A.P.CARTER,C.VONRHEIN,T.HARTSCH,V.RAMAKRISHNAN REMARK 1 TITL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT REMARK 1 REF NATURE V. 407 327 2000 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 11014170 REMARK 1 DOI 10.1038/35030006 REMARK 2 REMARK 2 RESOLUTION. 12.50 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 : 1J5E REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : X-RAY COORDINATES OF T. REMARK 3 THERMOPHILUS 30S RIBOSOMAL REMARK 3 SUBUNIT AND THE HOMOLOGY MODEL OF REMARK 3 T. THERMOPHILUS RBFA WERE FITTED REMARK 3 INTO THE 12.5 ANGSTROMS REMARK 3 RESOLUTION CRYO-EM MAP OF THE T. REMARK 3 THERMOPHILUS 30S SUBUNIT-RBFA REMARK 3 COMPLEX. ALL THE ATOMIC REMARK 3 COORDINATES WERE FITTED AS RIGID REMARK 3 BODIES REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--CROSS-CORRELATION BASED MANUAL FITTING REMARK 3 IN O REFINEMENT PROTOCOL--MULTIPLE RIGID BODY 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) : 12.50 REMARK 3 NUMBER OF PARTICLES : 61207 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: THIS ENTRY CONTAINS ONLY A CA TRACE FOR THE PROTEIN REMARK 3 AND ONLY PHOSPHORUS ATOM FOR THE RNA IN THE COORDINATE. CROSS- REMARK 3 CORRELATION COEFFICIENT (CCF) VALUE FOR RBFA HOMOLOGY MODEL REMARK 3 FITTED INTO THE CORRESPONDING CRYO-EM DENSITY WAS 0.79 REMARK 4 REMARK 4 2R1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1000044306. 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 : THERMUS THERMOPHILUS 30S REMARK 245 RIBOSOMAL SUBUNIT COMPLEXED REMARK 245 WITH RBFA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLEY-CRBON FILM REMARK 245 GRID REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : 20MM, HEPES-KOH (PH 7.8), 10MM REMARK 245 MG(OAC)2, 200MM NH4CL, 65MM KCL REMARK 245 PH : 7.80 REMARK 245 SAMPLE DETAILS : RBFA WAS BOUND TO S1-DEPLETED REMARK 245 30S SUBUNIT REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 18-JAN-05 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 700.00 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) : 2000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 50760 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : ZEISS IMAGING SCANNER, STEP REMARK 245 SIZE 14MICRO-M 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: DECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, X, F, G, H, I 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: 1J5E RELATED DB: PDB REMARK 900 30S X-RAY CRYSTALLOGRAPHIC STRUCTURE REMARK 900 RELATED ID: 2R1C RELATED DB: PDB REMARK 900 RBFA HOMOLOGY MODEL FITTED INTO 30S-RBFA CRYO-EM MAP REMARK 900 RELATED ID: 2DYJ RELATED DB: PDB REMARK 900 RBFA X-RAY CRYSTALLOGRAPHIC STRUCTURE REMARK 900 RELATED ID: EMD-1413 RELATED DB: EMDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SICNE THE PORTION (1411-1489) OF H44 IS NOT CLOSE TO THE RBFA, THE REMARK 999 AUTHOR DID NOT PROVIDE THOSE COORDINATES. THE AUTHOR ONLY PROVIDED REMARK 999 THE COORDINATES OF THE PORTION OF THE H44 (CHAINS E AND X) THAT IS REMARK 999 CLOSE TO THE RBFA. DBREF 2R1G G 2 128 UNP P62669 RS9_THET2 2 128 DBREF 2R1G H 5 128 UNP P17293 RS12_THETH 2 125 DBREF 2R1G I 2 126 UNP P62655 RS13_THET2 2 126 DBREF 2R1G A 6 29 PDB 2R1G 2R1G 6 29 DBREF 2R1G B 500 547 PDB 2R1G 2R1G 500 547 DBREF 2R1G C 885 913 PDB 2R1G 2R1G 885 913 DBREF 2R1G D 918 945 PDB 2R1G 2R1G 918 945 DBREF 2R1G E 1400 1410 PDB 2R1G 2R1G 1400 1410 DBREF 2R1G X 1490 1500 PDB 2R1G 2R1G 1490 1500 DBREF 2R1G F 1501 1529 PDB 2R1G 2R1G 1501 1529 SEQRES 1 A 24 G G A G A G U U U G A U C SEQRES 2 A 24 C U G G C U C A G G G SEQRES 1 B 48 G C G C C G G C C A A C U SEQRES 2 B 48 C C G U G C C A G C A G C SEQRES 3 B 48 C G C G G U A A U A C G G SEQRES 4 B 48 A G G G C G C G A SEQRES 1 C 29 G G G G A G U A C G G C C SEQRES 2 C 29 G C A A G G C U G A A A C SEQRES 3 C 29 U C A SEQRES 1 D 28 A A U U G A C G G G G G C SEQRES 2 D 28 C G C C U U G U A C A C A SEQRES 3 D 28 C C SEQRES 1 E 11 C G C C C G U C A C G SEQRES 1 X 11 C G A A G U C G U A A SEQRES 1 F 29 C A A G G U A G C U G U A SEQRES 2 F 29 C C G G A A G G U G C G G SEQRES 3 F 29 C U G SEQRES 1 G 127 GLU GLN TYR TYR GLY THR GLY ARG ARG LYS GLU ALA VAL SEQRES 2 G 127 ALA ARG VAL PHE LEU ARG PRO GLY ASN GLY LYS VAL THR SEQRES 3 G 127 VAL ASN GLY GLN ASP PHE ASN GLU TYR PHE GLN GLY LEU SEQRES 4 G 127 VAL ARG ALA VAL ALA ALA LEU GLU PRO LEU ARG ALA VAL SEQRES 5 G 127 ASP ALA LEU GLY ARG PHE ASP ALA TYR ILE THR VAL ARG SEQRES 6 G 127 GLY GLY GLY LYS SER GLY GLN ILE ASP ALA ILE LYS LEU SEQRES 7 G 127 GLY ILE ALA ARG ALA LEU VAL GLN TYR ASN PRO ASP TYR SEQRES 8 G 127 ARG ALA LYS LEU LYS PRO LEU GLY PHE LEU THR ARG ASP SEQRES 9 G 127 ALA ARG VAL VAL GLU ARG LYS LYS TYR GLY LYS HIS LYS SEQRES 10 G 127 ALA ARG ARG ALA PRO GLN TYR SER LYS ARG SEQRES 1 H 124 PRO THR ILE ASN GLN LEU VAL ARG LYS GLY ARG GLU LYS SEQRES 2 H 124 VAL ARG LYS LYS SER LYS VAL PRO ALA LEU LYS GLY ALA SEQRES 3 H 124 PRO PHE ARG ARG GLY VAL CYS THR VAL VAL ARG THR VAL SEQRES 4 H 124 THR PRO LYS LYS PRO ASN SER ALA LEU ARG LYS VAL ALA SEQRES 5 H 124 LYS VAL ARG LEU THR SER GLY TYR GLU VAL THR ALA TYR SEQRES 6 H 124 ILE PRO GLY GLU GLY HIS ASN LEU GLN GLU HIS SER VAL SEQRES 7 H 124 VAL LEU ILE ARG GLY GLY ARG VAL LYS ASP LEU PRO GLY SEQRES 8 H 124 VAL ARG TYR HIS ILE VAL ARG GLY VAL TYR ASP ALA ALA SEQRES 9 H 124 GLY VAL LYS ASP ARG LYS LYS SER ARG SER LYS TYR GLY SEQRES 10 H 124 THR LYS LYS PRO LYS GLU ALA SEQRES 1 I 125 ALA ARG ILE ALA GLY VAL GLU ILE PRO ARG ASN LYS ARG SEQRES 2 I 125 VAL ASP VAL ALA LEU THR TYR ILE TYR GLY ILE GLY LYS SEQRES 3 I 125 ALA ARG ALA LYS GLU ALA LEU GLU LYS THR GLY ILE ASN SEQRES 4 I 125 PRO ALA THR ARG VAL LYS ASP LEU THR GLU ALA GLU VAL SEQRES 5 I 125 VAL ARG LEU ARG GLU TYR VAL GLU ASN THR TRP LYS LEU SEQRES 6 I 125 GLU GLY GLU LEU ARG ALA GLU VAL ALA ALA ASN ILE LYS SEQRES 7 I 125 ARG LEU MET ASP ILE GLY CYS TYR ARG GLY LEU ARG HIS SEQRES 8 I 125 ARG ARG GLY LEU PRO VAL ARG GLY GLN ARG THR ARG THR SEQRES 9 I 125 ASN ALA ARG THR ARG LYS GLY PRO ARG LYS THR VAL ALA SEQRES 10 I 125 GLY LYS LYS LYS ALA PRO ARG LYS 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