10 20 30 40 50 60 70 80 2R1G - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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: 30S RIBOSOMAL PROTEIN S9; COMPND 3 CHAIN: G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 30S RIBOSOMAL PROTEIN S12; COMPND 7 CHAIN: H; COMPND 8 FRAGMENT: RESIDUES 5-128; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 30S RIBOSOMAL PROTEIN S13; COMPND 12 CHAIN: I; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: 16S RIBOSOMAL RNA HELIX 1; COMPND 16 CHAIN: A; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 5; COMPND 19 MOLECULE: 16S RIBOSOMAL RNA HELIX 18; COMPND 20 CHAIN: B; COMPND 21 ENGINEERED: YES; COMPND 22 MOL_ID: 6; COMPND 23 MOLECULE: 16S RIBOSOMAL RNA HELIX 27; COMPND 24 CHAIN: C; COMPND 25 ENGINEERED: YES; COMPND 26 MOL_ID: 7; COMPND 27 MOLECULE: 16S RIBOSOMAL RNA HELIX 28; COMPND 28 CHAIN: D; COMPND 29 ENGINEERED: YES; COMPND 30 MOL_ID: 8; COMPND 31 MOLECULE: 16S RIBOSOMAL RNA HELIX 44; COMPND 32 CHAIN: E; COMPND 33 ENGINEERED: YES; COMPND 34 MOL_ID: 9; COMPND 35 MOLECULE: 16S RIBOSOMAL RNA HELIX 44; COMPND 36 CHAIN: X; COMPND 37 ENGINEERED: YES; COMPND 38 MOL_ID: 10; COMPND 39 MOLECULE: 16S RIBOSOMAL RNA HELIX 45; COMPND 40 CHAIN: F; COMPND 41 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 GENE: RPSI, RPS9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 10 ORGANISM_TAXID: 262724; SOURCE 11 STRAIN: HB27; SOURCE 12 GENE: RPSL, RPS12; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 17 ORGANISM_TAXID: 262724; SOURCE 18 STRAIN: HB27; SOURCE 19 GENE: RPSM, RPS13; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 SYNTHETIC: YES; SOURCE 24 MOL_ID: 5; SOURCE 25 SYNTHETIC: YES; SOURCE 26 MOL_ID: 6; SOURCE 27 SYNTHETIC: YES; SOURCE 28 MOL_ID: 7; SOURCE 29 SYNTHETIC: YES; SOURCE 30 MOL_ID: 8; SOURCE 31 SYNTHETIC: YES; SOURCE 32 MOL_ID: 9; SOURCE 33 SYNTHETIC: YES; SOURCE 34 MOL_ID: 10; SOURCE 35 SYNTHETIC: YES
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 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 : MANUAL REMARK 3 RECONSTRUCTION SCHEMA : CRYO-ELECTRON MICROSCOPY AND 3D IMAGE REMARK 3 PROCESSING REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1J5E REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : MULTIPLE RIGID BODY REMARK 3 REFINEMENT TARGET : X-RAY COORDINATES OF T. REMARK 3 THERMOPHILUS 30S RIBOSOMAL SUBUNIT REMARK 3 AND THE HOMOLOGY MODEL OF T. REMARK 3 THERMOPHILUS RBFA WERE FITTED INTO REMARK 3 THE 12.5 ANGSTROMS RESOLUTION CRYO REMARK 3 -EM MAP OF THE T. THERMOPHILUS 30S REMARK 3 SUBUNIT-RBFA COMPLEX. ALL THE REMARK 3 ATOMIC COORDINATES WERE FITTED AS REMARK 3 RIGID BODIES REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : CROSS-CORRELATION BASED MANUAL FITTING IN 'O' REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : 2.760 REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 12.500 REMARK 3 NUMBER OF PARTICLES : 61207 REMARK 3 CTF CORRECTION METHOD : CTF CORRECTION OF 3D-MAPS BY REMARK 3 WIENER FILTRATION 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 ON 19-SEP-07. REMARK 100 THE RCSB ID CODE IS RCSB044306.
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 : THERMUS THERMOPHILUS 30S REMARK 245 RIBOSOMAL SUBUNIT COMPLEXED WITH REMARK 245 RBFA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLEY-CRBON FILM 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 : 131 REMARK 245 TEMPERATURE (KELVIN) : 93.00 REMARK 245 MICROSCOPE MODEL : PHILIPS TECNAI F20 EFG REMARK 245 DETECTOR TYPE : KODAK S0163 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 : FEG 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 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: 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 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 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
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