PDB Short entry for 1X1L HEADER STRUCTURAL PROTEIN/RNA 06-APR-05 1X1L TITLE INTERACTION OF ERA,A GTPASE PROTEIN, WITH THE 3'MINOR DOMAIN OF THE TITLE 2 16S RRNA WITHIN THE THERMUS THERMOPHILUS 30S SUBUNIT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (130-MER); COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: GTP-BINDING PROTEIN ERA; COMPND 6 CHAIN: X SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 6 ORGANISM_TAXID: 562 KEYWDS INTERACTION OF ERA PROTEIN WITH THE 3'MINOR DOMAIN OF 16S RRNA, KEYWDS 2 STRUCTURAL PROTEIN-RNA COMPLEX EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN X; P ATOMS ONLY, CHAIN A AUTHOR M.R.SHARMA,C.BARAT,R.K.AGRAWAL REVDAT 4 13-MAR-24 1X1L 1 REMARK REVDAT 3 18-DEC-19 1X1L 1 REMARK REVDAT 2 24-FEB-09 1X1L 1 VERSN REVDAT 1 17-MAY-05 1X1L 0 JRNL AUTH M.R.SHARMA,C.BARAT,D.N.WILSON,T.M.BOOTH,M.KAWAZOE, JRNL AUTH 2 C.HORI-TAKEMOTO,M.SHIROUZU,S.YOKOYAMA,P.FUCINI,R.K.AGRAWAL JRNL TITL INTERACTION OF ERA WITH THE 30S RIBOSOMAL SUBUNIT JRNL TITL 2 IMPLICATIONS FOR 30S SUBUNIT ASSEMBLY JRNL REF MOL.CELL V. 18 319 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 15866174 JRNL DOI 10.1016/J.MOLCEL.2005.03.028 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.T.WIMBERLY,D.E.BRODERSEN,W.M.CLEMONS JR., REMARK 1 AUTH 2 R.J.MORGAN-WARREN,A.P.CARTER,C.VONRHEIN,T.HARTSCH, REMARK 1 AUTH 3 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 1 REFERENCE 2 REMARK 1 AUTH X.CHEN,D.L.COURT,X.JI REMARK 1 TITL CRYSTAL STRUCTURE OF ERA: A GTPASE-DEPENDENT CELL CYCLE REMARK 1 TITL 2 REGULATOR CONTAINING AN RNA BINDING MOTIF REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 96 8396 1999 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 10411886 REMARK 1 DOI 10.1073/PNAS.96.15.8396 REMARK 1 REFERENCE 3 REMARK 1 AUTH M.KAWAZOE,C.TAKEMOTO,T.KAMINISHI,S.SEKINE,M.SHIROUZU, REMARK 1 AUTH 2 P.FUCINI,R.K.AGRAWAL,S.YOKOYAMA REMARK 1 TITL CRYSTAL STRUCTURE OF ERA FROM THERMUS THERMOPHILUS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 13.50 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 : 1FJF REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : X-RAY COORDINATES OF THE 30S REMARK 3 RIBOSOMAL SUBUNIT AND ERA WERE REMARK 3 FITTED INTO THE 13.5 ANGSTROMS REMARK 3 RESOLUTION CRYO-EM MAP OF THE T. REMARK 3 THERMOPHILUS 30S SUBUNIT-ERA REMARK 3 COMPLEX. THE ATOMIC STRUCTURE OF REMARK 3 ERA WAS FITTED AS 3 RIGID BODIES, REMARK 3 N-TERMINAL DOMAIN, C-TERMINAL REMARK 3 DOMAIN AND C-TERMINAL HELIX REMARK 3 WITHIN THE C-TERMINAL DOMAIN. THE REMARK 3 RESULTANT ERA STRUCTURE WAS THEN REMARK 3 ENERGY MINIMIZED. THE X-RAY REMARK 3 COORDINATES OF T. THERMOPHILUS REMARK 3 30S SUBUNIT WAS FITTED AS 4 RIGID REMARK 3 BODIES, HEAD, BODY, PLATFORM AND REMARK 3 16S RRNA 3' MINOR DOMAINS. ONLY REMARK 3 THE COORDINATES OF THE 16S RRNA 3' REMARK 3 MINOR DOMAIN AND ERA ARE REMARK 3 INCLUDED HERE. THE KH DOMAIN OF REMARK 3 ERA MAKES DIRECT CONTACT WITH THE REMARK 3 3' TERMINUS OF THE 16S RRNA. 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) : 13.50 REMARK 3 NUMBER OF PARTICLES : NULL REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: TMV REMARK 3 REMARK 3 OTHER DETAILS: PROJECTION MATCHING USING SPIDER PACKAGE. THE REMARK 3 COORDINATES FOR ONLY THE ALPHA CARBONS IN PROTEIN AND REMARK 3 PHOSPHORUSES IN RRNA ARE PRESENT IN THE STRUCTURE. THE NUMBER OF REMARK 3 MISSING ATOMS WAS SO MUCH THAT REMARK 470 FOR THE MISSING ATOMS REMARK 3 LIST WERE REMOVED. REMARK 4 REMARK 4 1X1L 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_1000024263. 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 ERA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.03 REMARK 245 SAMPLE SUPPORT DETAILS : QUANTIFOIL HOLLEY-CARBON FILM REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : RAPID-FREEZING IN LIQUID ETHANE REMARK 245 SAMPLE BUFFER : HEPES-KOH REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : ERA WAS BOUND TO A S1-DEPLETED REMARK 245 30S SUBUNIT REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 25-MAR-03 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) : 1180.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3940.00 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 : 49696 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 APPLY THE FOLLOWING TO CHAINS: A, X 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 MET X 1 REMARK 465 SER X 2 REMARK 465 ILE X 3 REMARK 465 GLY X 296 REMARK 465 TYR X 297 REMARK 465 VAL X 298 REMARK 465 ASP X 299 REMARK 465 ASP X 300 REMARK 465 LEU X 301 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 531 CA ASN X 249 0.75 REMARK 500 P G A 422 P C A 477 1.91 REMARK 500 P A A 534 CA LYS X 255 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FJF RELATED DB: PDB REMARK 900 STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT REMARK 900 RELATED ID: 1EGA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ERA: A GTPASE-DEPENDENT CELL CYCLE REGULATOR REMARK 900 CONTAINING AN RNA BINDING MOTIF REMARK 900 RELATED ID: 1WF3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ERA FROM THERMUS THERMOPHILUS (IN PREPARATION) REMARK 900 RELATED ID: 1X18 RELATED DB: PDB REMARK 900 CONTACT SITES OF ERA GTPASE ON THE THERMUS THERMOPHILUS 30S SUBUNIT DBREF 1X1L X 1 301 UNP P06616 ERA_ECOLI 1 301 DBREF 1X1L A 400 534 PDB 1X1L 1X1L 400 534 SEQRES 1 A 130 C G C C C G U C A C G C C SEQRES 2 A 130 A U G G G A G C G G G C U SEQRES 3 A 130 C U A C C C G A A G U C G SEQRES 4 A 130 C C G G G A G C C U A C G SEQRES 5 A 130 G G C A G G C G C C G A G SEQRES 6 A 130 G G U A G G G C C C G U G SEQRES 7 A 130 A C U G G G G C G A A G U SEQRES 8 A 130 C G U A A C A A G G U A G SEQRES 9 A 130 C U G U A C C G G A A G G SEQRES 10 A 130 U G C G G C U G G A U C A SEQRES 1 X 301 MET SER ILE ASP LYS SER TYR CYS GLY PHE ILE ALA ILE SEQRES 2 X 301 VAL GLY ARG PRO ASN VAL GLY LYS SER THR LEU LEU ASN SEQRES 3 X 301 LYS LEU LEU GLY GLN LYS ILE SER ILE THR SER ARG LYS SEQRES 4 X 301 ALA GLN THR THR ARG HIS ARG ILE VAL GLY ILE HIS THR SEQRES 5 X 301 GLU GLY ALA TYR GLN ALA ILE TYR VAL ASP THR PRO GLY SEQRES 6 X 301 LEU HIS MET GLU GLU LYS ARG ALA ILE ASN ARG LEU MET SEQRES 7 X 301 ASN LYS ALA ALA SER SER SER ILE GLY ASP VAL GLU LEU SEQRES 8 X 301 VAL ILE PHE VAL VAL GLU GLY THR ARG TRP THR PRO ASP SEQRES 9 X 301 ASP GLU MET VAL LEU ASN LYS LEU ARG GLU GLY LYS ALA SEQRES 10 X 301 PRO VAL ILE LEU ALA VAL ASN LYS VAL ASP ASN VAL GLN SEQRES 11 X 301 GLU LYS ALA ASP LEU LEU PRO HIS LEU GLN PHE LEU ALA SEQRES 12 X 301 SER GLN MET ASN PHE LEU ASP ILE VAL PRO ILE SER ALA SEQRES 13 X 301 GLU THR GLY LEU ASN VAL ASP THR ILE ALA ALA ILE VAL SEQRES 14 X 301 ARG LYS HIS LEU PRO GLU ALA THR HIS HIS PHE PRO GLU SEQRES 15 X 301 ASP TYR ILE THR ASP ARG SER GLN ARG PHE MET ALA SER SEQRES 16 X 301 GLU ILE ILE ARG GLU LYS LEU MET ARG PHE LEU GLY ALA SEQRES 17 X 301 GLU LEU PRO TYR SER VAL THR VAL GLU ILE GLU ARG PHE SEQRES 18 X 301 VAL SER ASN GLU ARG GLY GLY TYR ASP ILE ASN GLY LEU SEQRES 19 X 301 ILE LEU VAL GLU ARG GLU GLY GLN LYS LYS MET VAL ILE SEQRES 20 X 301 GLY ASN LYS GLY ALA LYS ILE LYS THR ILE GLY ILE GLU SEQRES 21 X 301 ALA ARG LYS ASP MET GLN GLU MET PHE GLU ALA PRO VAL SEQRES 22 X 301 HIS LEU GLU LEU TRP VAL LYS VAL LYS SER GLY TRP ALA SEQRES 23 X 301 ASP ASP GLU ARG ALA LEU ARG SER LEU GLY TYR VAL ASP SEQRES 24 X 301 ASP 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