PDB Short entry for 2IY3 HEADER RNA-BINDING 12-JUL-06 2IY3 TITLE STRUCTURE OF THE E. COLI SIGNAL REGOGNITION PARTICLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL RECOGNITION PARTICLE PROTEIN,SIGNAL RECOGNITION COMPND 3 PARTICLE 54 KDA PROTEIN; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: FIFTY-FOUR HOMOLOG,SRP54; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 4.5S RNA; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: SIGNAL SEQUENCE; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS, SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 271, 2287; SOURCE 4 GENE: FFH, SRP54, SULA_1982, SULB_1983, SULC_1981; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A_FFH; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630 KEYWDS RNA-BINDING, RNA-BINDING PROTEIN COMPLEX, SIGNAL RECOGNITION PARTICLE EXPDTA ELECTRON MICROSCOPY MDLTYP CA ATOMS ONLY, CHAIN A, C ; P ATOMS ONLY, CHAIN B AUTHOR C.SCHAFFITZEL,M.OSWALD,I.BERGER,T.ISHIKAWA,J.P.ABRAHAMS,H.K.KOERTEN, AUTHOR 2 R.I.KONING,N.BAN REVDAT 6 23-AUG-17 2IY3 1 REMARK REVDAT 5 15-MAR-17 2IY3 1 SOURCE REVDAT 4 07-AUG-13 2IY3 1 REMARK VERSN CRYST1 SCALE1 REVDAT 4 2 1 SCALE2 SCALE3 REVDAT 3 24-FEB-09 2IY3 1 VERSN REVDAT 2 21-NOV-06 2IY3 1 JRNL DBREF REVDAT 1 02-NOV-06 2IY3 0 JRNL AUTH C.SCHAFFITZEL,M.OSWALD,I.BERGER,T.ISHIKAWA,J.P.ABRAHAMS, JRNL AUTH 2 H.K.KOERTEN,R.I.KONING,N.BAN JRNL TITL STRUCTURE OF THE E. COLI SIGNAL RECOGNITION PARTICLE BOUND JRNL TITL 2 TO A TRANSLATING RIBOSOME JRNL REF NATURE V. 444 503 2006 JRNL REFN ISSN 0028-0836 JRNL PMID 17086205 JRNL DOI 10.1038/NATURE05182 REMARK 2 REMARK 2 RESOLUTION. 16.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NOMAD, SPIDER REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1JPN REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL- REMARK 3 -X-RAY REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 3.810 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 16.00 REMARK 3 NUMBER OF PARTICLES : 24382 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THE COORDINATES BELOW ARE MADE UP FROM THE REMARK 3 FOLLOWING COMPONENTS: FFH NG DOMAIN (RESIDUE 1-296), ORGANISM REMARK 3 SCIENTIFIC: THERMUS AQUATICUS (PDB ENTRY 1JPN CHAIN A). FFH M REMARK 3 DOMAIN (RESIDUE 297-432), ORANISM SCIENTIFIC: SULFOLOBUS REMARK 3 SOLFATARICUS (PDB ENTRY 1QZW CHAIN A). 4.5S RNA (RESIDUE 33- 73), REMARK 3 ORGANISM SCIENTIFIC: SULFOLOBUS SOLFATARICUS (PDB ENTRY 1QZW, REMARK 3 CHAIN B). 4.5S RNA (RESIDUE 1-32 AND 74-110), ORGANISM REMARK 3 SCIENTIFIC: ESCHERICHIA COLI (PDB: SRPDB, ROSENBLAD ET AL, REMARK 3 NUCLEIC ACID RES 21, 363-364,12:2003. REMARK 4 REMARK 4 2IY3 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_1290029361. 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 : SRP BOUND TO RIBOSOME REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : HOLEY CARBON REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO ETHANE REMARK 245 SAMPLE BUFFER : 50 MM HEPES-KOH PH 7.5, 100 MM REMARK 245 KCL, 25 MM MGCL2, 1 MM DTT,1 MM REMARK 245 GTP REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 02-JUN-05 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 77.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI 20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4500.00 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) : 10.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 51000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-1250 RELATED DB: EMDB REMARK 900 STRUCTURE OF THE E. COLI SIGNAL RECOGNITION PARTICLE BOUND TO A REMARK 900 TRANSLATING RIBOSOME VOLUME DATA DBREF 2IY3 A 1 296 UNP O07347 SRP54_THEAQ 1 296 DBREF1 2IY3 A 297 432 UNP A0A0E3MG81_SULSF DBREF2 2IY3 A A0A0E3MG81 297 432 DBREF1 2IY3 B 1 110 GB LT615377.1 DBREF2 2IY3 B 1126835767 475747 475856 DBREF 2IY3 C 450 466 PDB 2IY3 2IY3 450 466 SEQADV 2IY3 A B 54 GB 112683576 G 75800 CONFLICT SEQRES 1 A 432 MET PHE GLN GLN LEU SER ALA ARG LEU GLN GLU ALA ILE SEQRES 2 A 432 GLY ARG LEU ARG GLY ARG GLY ARG ILE THR GLU GLU ASP SEQRES 3 A 432 LEU LYS ALA THR LEU ARG GLU ILE ARG ARG ALA LEU MET SEQRES 4 A 432 ASP ALA ASP VAL ASN LEU GLU VAL ALA ARG ASP PHE VAL SEQRES 5 A 432 GLU ARG VAL ARG GLU GLU ALA LEU GLY LYS GLN VAL LEU SEQRES 6 A 432 GLU SER LEU THR PRO ALA GLU VAL ILE LEU ALA THR VAL SEQRES 7 A 432 TYR GLU ALA LEU LYS GLU ALA LEU GLY GLY GLU ALA ARG SEQRES 8 A 432 LEU PRO VAL LEU LYS ASP ARG ASN LEU TRP PHE LEU VAL SEQRES 9 A 432 GLY LEU GLN GLY SER GLY LYS THR THR THR ALA ALA LYS SEQRES 10 A 432 LEU ALA LEU TYR TYR LYS GLY LYS GLY ARG ARG PRO LEU SEQRES 11 A 432 LEU VAL ALA ALA ASP THR GLN ARG PRO ALA ALA ARG GLU SEQRES 12 A 432 GLN LEU ARG LEU LEU GLY GLU LYS VAL GLY VAL PRO VAL SEQRES 13 A 432 LEU GLU VAL MET ASP GLY GLU SER PRO GLU SER ILE ARG SEQRES 14 A 432 ARG ARG VAL GLU GLU LYS ALA ARG LEU GLU ALA ARG ASP SEQRES 15 A 432 LEU ILE LEU VAL ASP THR ALA GLY ARG LEU GLN ILE ASP SEQRES 16 A 432 GLU PRO LEU MET GLY GLU LEU ALA ARG LEU LYS GLU VAL SEQRES 17 A 432 LEU GLY PRO ASP GLU VAL LEU LEU VAL LEU ASP ALA MET SEQRES 18 A 432 THR GLY GLN GLU ALA LEU SER VAL ALA ARG ALA PHE ASP SEQRES 19 A 432 GLU LYS VAL GLY VAL THR GLY LEU VAL LEU THR LYS LEU SEQRES 20 A 432 ASP GLY ASP ALA ARG GLY GLY ALA ALA LEU SER ALA ARG SEQRES 21 A 432 HIS VAL THR GLY LYS PRO ILE TYR PHE ALA GLY VAL SER SEQRES 22 A 432 GLU LYS PRO GLU GLY LEU GLU PRO PHE TYR PRO GLU ARG SEQRES 23 A 432 LEU ALA GLY ARG ILE LEU GLY MET GLY ASP ILE GLU SER SEQRES 24 A 432 ILE LEU GLU LYS VAL LYS GLY LEU GLU GLU TYR ASP LYS SEQRES 25 A 432 ILE GLN LYS LYS MET GLU ASP VAL MET GLU GLY LYS GLY SEQRES 26 A 432 LYS LEU THR LEU ARG ASP VAL TYR ALA GLN ILE ILE ALA SEQRES 27 A 432 LEU ARG LYS MET GLY PRO LEU SER LYS VAL LEU GLN HIS SEQRES 28 A 432 ILE PRO GLY LEU GLY ILE MET LEU PRO THR PRO SER GLU SEQRES 29 A 432 ASP GLN LEU LYS ILE GLY GLU GLU LYS ILE ARG ARG TRP SEQRES 30 A 432 LEU ALA ALA LEU ASN SER MET THR TYR LYS GLU LEU GLU SEQRES 31 A 432 ASN PRO ASN ILE ILE ASP LYS SER ARG MET ARG ARG ILE SEQRES 32 A 432 ALA GLU GLY SER GLY LEU GLU VAL GLU GLU VAL ARG GLU SEQRES 33 A 432 LEU LEU GLU TRP TYR ASN ASN MET ASN ARG LEU LEU LYS SEQRES 34 A 432 MET VAL LYS SEQRES 1 B 110 G G G G G C U C U G U U G SEQRES 2 B 110 G U U C U C C C G C A A C SEQRES 3 B 110 G C U A C U C U G U U U A SEQRES 4 B 110 C C A G G U C A G G U C C SEQRES 5 B 110 G A A A G G A A G C A G C SEQRES 6 B 110 C A A G G C A G A U G A C SEQRES 7 B 110 G C G U G U G C C G G G A SEQRES 8 B 110 U G U A G C U G G C A G G SEQRES 9 B 110 G C C C C C SEQRES 1 C 17 ALA ALA LEU ALA LEU ALA ALA ALA ALA ALA LEU ALA LEU SEQRES 2 C 17 ALA ALA ALA GLY 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